Method for Using Gene Expression to Determine Prognosis of Prostate Cancer

ABSTRACT

Molecular assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for said patient, and likelihood that said patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status, are provided herein.

This application is a continuation of U.S. application Ser. No. 14/887,605, filed Oct. 20, 2015, which is a continuation of U.S. application Ser. No. 13/190,391, filed Jul. 25, 2011, which claims the benefit of priority to U.S. Provisional Application Nos. 61/368,217, filed Jul. 27, 2010; 61/414,310, filed Nov. 16, 2010; and 61/485,536, filed May 12, 2011, all of which are hereby incorporated by reference.

TECHNICAL FIELD

The present disclosure relates to molecular diagnostic assays that provide information concerning methods to use gene expression profiles to determine prognostic information for cancer patients. Specifically, the present disclosure provides genes and microRNAs, the expression levels of which may be used to determine the likelihood that a prostate cancer patient will experience a local or distant cancer recurrence.

INTRODUCTION

Prostate cancer is the most common solid malignancy in men and the second most common cause of cancer-related death in men in North America and the European Union (EU). In 2008, over 180,000 patients will be diagnosed with prostate cancer in the United States alone and nearly 30,000 will die of this disease. Age is the single most important risk factor for the development of prostate cancer, and applies across all racial groups that have been studied. With the aging of the U.S. population, it is projected that the annual incidence of prostate cancer will double by 2025 to nearly 400,000 cases per year.

Since the introduction of prostate-specific antigen (PSA) screening in the 1990's, the proportion of patients presenting with clinically evident disease has fallen dramatically such that patients categorized as “low risk” now constitute half of new diagnoses today. PSA is used as a tumor marker to determine the presence of prostate cancer as high PSA levels are associated with prostate cancer. Despite a growing proportion of localized prostate cancer patients presenting with low-risk features such as low stage (T1) disease, greater than 90% of patients in the US still undergo definitive therapy, including prostatectomy or radiation. Only about 15% of these patients would develop metastatic disease and die from their prostate cancer, even in the absence of definitive therapy. A. Bill-Axelson, et al., J Nat'l Cancer Inst. 100(16):1144-1154 (2008). Therefore, the majority of prostate cancer patients are being over-treated.

Estimates of recurrence risk and treatment decisions in prostate cancer are currently based primarily on PSA levels and/or tumor stage. Although tumor stage has been demonstrated to have significant association with outcome sufficient to be included in pathology reports, the College of American Pathologists Consensus Statement noted that variations in approach to the acquisition, interpretation, reporting, and analysis of this information exist. C. Compton, et al., Arch Pathol Lab Med 124:979-992 (2000). As a consequence, existing pathologic staging methods have been criticized as lacking reproducibility and therefore may provide imprecise estimates of individual patient risk.

SUMMARY

This application discloses molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of cancer recurrence. For example, the likelihood of cancer recurrence could be described in terms of a score based on clinical or biochemical recurrence-free interval.

In addition, this application discloses molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained to identify a risk classification for a prostate cancer patient. For example, patients may be stratified using expression level(s) of one or more genes or microRNAs associated, positively or negatively, with cancer recurrence or death from cancer, or with a prognostic factor. In an exemplary embodiment, the prognostic factor is Gleason pattern.

The biological sample may be obtained from standard methods, including surgery, biopsy, or bodily fluids. It may comprise tumor tissue or cancer cells, and, in some cases, histologically normal tissue, e.g., histologically normal tissue adjacent the tumor tissue. In exemplary embodiments, the biological sample is positive or negative for a TMPRSS2 fusion.

In exemplary embodiments, expression level(s) of one or more genes and/or microRNAs that are associated, positively or negatively, with a particular clinical outcome in prostate cancer are used to determine prognosis and appropriate therapy. The genes disclosed herein may be used alone or arranged in functional gene subsets, such as cell adhesion/migration, immediate-early stress response, and extracellular matrix-associated. Each gene subset comprises the genes disclosed herein, as well as genes that are co-expressed with one or more of the disclosed genes. The calculation may be performed on a computer, programmed to execute the gene expression analysis. The microRNAs disclosed herein may also be used alone or in combination with any one or more of the microRNAs and/or genes disclosed.

In exemplary embodiments, the molecular assay may involve expression levels for at least two genes. The genes, or gene subsets, may be weighted according to strength of association with prognosis or tumor microenvironment. In another exemplary embodiment, the molecular assay may involve expression levels of at least one gene and at least one microRNA. The gene-microRNA combination may be selected based on the likelihood that the gene-microRNA combination functionally interact.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows the distribution of clinical and pathology assessments of biopsy Gleason score, baseline PSA level, and clinical T-stage.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), and March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992), provide one skilled in the art with a general guide to many of the terms used in the present application.

One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Indeed, the present invention is in no way limited to the methods and materials described herein. For purposes of the invention, the following terms are defined below.

The terms “tumor” and “lesion” as used herein, refer to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. Those skilled in the art will realize that a tumor tissue sample may comprise multiple biological elements, such as one or more cancer cells, partial or fragmented cells, tumors in various stages, surrounding histologically normal-appearing tissue, and/or macro or micro-dissected tissue.

The terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer in the present disclosure include cancer of the urogenital tract, such as prostate cancer.

The “pathology” of cancer includes all phenomena that compromise the well-being of the patient. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc.

As used herein, the term “prostate cancer” is used interchangeably and in the broadest sense refers to all stages and all forms of cancer arising from the tissue of the prostate gland.

According to the tumor, node, metastasis (TNM) staging system of the American Joint Committee on Cancer (AJCC), AJCC Cancer Staging Manual (7th Ed., 2010), the various stages of prostate cancer are defined as follows: Tumor: T1: clinically inapparent tumor not palpable or visible by imaging, T1a: tumor incidental histological finding in 5% or less of tissue resected, T1b: tumor incidental histological finding in more than 5% of tissue resected, T1c: tumor identified by needle biopsy; T2: tumor confined within prostate, T2a: tumor involves one half of one lobe or less, T2b: tumor involves more than half of one lobe, but not both lobes, T2c: tumor involves both lobes; T3: tumor extends through the prostatic capsule, T3a: extracapsular extension (unilateral or bilateral), T3b: tumor invades seminal vesicle(s); T4: tumor is fixed or invades adjacent structures other than seminal vesicles (bladder neck, external sphincter, rectum, levator muscles, or pelvic wall). Node: N0: no regional lymph node metastasis; N1: metastasis in regional lymph nodes. Metastasis: M0: no distant metastasis; M1: distant metastasis present.

The Gleason Grading system is used to help evaluate the prognosis of men with prostate cancer. Together with other parameters, it is incorporated into a strategy of prostate cancer staging, which predicts prognosis and helps guide therapy. A Gleason “score” or “grade” is given to prostate cancer based upon its microscopic appearance. Tumors with a low Gleason score typically grow slowly enough that they may not pose a significant threat to the patients in their lifetimes. These patients are monitored (“watchful waiting” or “active surveillance”) over time. Cancers with a higher Gleason score are more aggressive and have a worse prognosis, and these patients are generally treated with surgery (e.g., radical prostectomy) and, in some cases, therapy (e.g., radiation, hormone, ultrasound, chemotherapy). Gleason scores (or sums) comprise grades of the two most common tumor patterns. These patterns are referred to as Gleason patterns 1-5, with pattern 1 being the most well-differentiated. Most have a mixture of patterns. To obtain a Gleason score or grade, the dominant pattern is added to the second most prevalent pattern to obtain a number between 2 and 10. The Gleason Grades include: G1: well differentiated (slight anaplasia) (Gleason 2-4); G2: moderately differentiated (moderate anaplasia) (Gleason 5-6); G3-4: poorly differentiated/undifferentiated (marked anaplasia) (Gleason 7-10).

Stage groupings: Stage I: T1a N0M0 G1; Stage II: (T1a N0 M0 G2-4) or (T1b, c, T1, T2, N0 M0 Any G); Stage III: T3 N0 M0 Any G; Stage IV: (T4 N0 M0 Any G) or (Any T N1 M0 Any G) or (Any T Any N M1 Any G).

As used herein, the term “tumor tissue” refers to a biological sample containing one or more cancer cells, or a fraction of one or more cancer cells. Those skilled in the art will recognize that such biological sample may additionally comprise other biological components, such as histologically appearing normal cells (e.g., adjacent the tumor), depending upon the method used to obtain the tumor tissue, such as surgical resection, biopsy, or bodily fluids.

As used herein, the term “AUA risk group” refers to the 2007 updated American Urological Association (AUA) guidelines for management of clinically localized prostate cancer, which clinicians use to determine whether a patient is at low, intermediate, or high risk of biochemical (PSA) relapse after local therapy.

As used herein, the term “adjacent tissue (AT)” refers to histologically “normal” cells that are adjacent a tumor. For example, the AT expression profile may be associated with disease recurrence and survival.

As used herein “non-tumor prostate tissue” refers to histologically normal-appearing tissue adjacent a prostate tumor.

Prognostic factors are those variables related to the natural history of cancer, which influence the recurrence rates and outcome of patients once they have developed cancer. Clinical parameters that have been associated with a worse prognosis include, for example, increased tumor stage, PSA level at presentation, and Gleason grade or pattern. Prognostic factors are frequently used to categorize patients into subgroups with different baseline relapse risks.

The term “prognosis” is used herein to refer to the likelihood that a cancer patient will have a cancer-attributable death or progression, including recurrence, metastatic spread, and drug resistance, of a neoplastic disease, such as prostate cancer. For example, a “good prognosis” would include long term survival without recurrence and a “bad prognosis” would include cancer recurrence.

As used herein, the term “expression level” as applied to a gene refers to the normalized level of a gene product, e.g. the normalized value determined for the RNA expression level of a gene or for the polypeptide expression level of a gene.

The term “gene product” or “expression product” are used herein to refer to the RNA (ribonucleic acid) transcription products (transcripts) of the gene, including mRNA, and the polypeptide translation products of such RNA transcripts. A gene product can be, for example, an unspliced RNA, an mRNA, a splice variant mRNA, a microRNA, a fragmented RNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide, etc.

The term “RNA transcript” as used herein refers to the RNA transcription products of a gene, including, for example, mRNA, an unspliced RNA, a splice variant mRNA, a microRNA, and a fragmented RNA.

The term “microRNA” is used herein to refer to a small, non-coding, single-stranded RNA of ˜18-25 nucleotides that may regulate gene expression. For example, when associated with the RNA-induced silencing complex (RISC), the complex binds to specific mRNA targets and causes translation repression or cleavage of these mRNA sequences.

Unless indicated otherwise, each gene name used herein corresponds to the Official Symbol assigned to the gene and provided by Entrez Gene (URL: www.ncbi.nlm.nih.gov/sites/entrez) as of the filing date of this application.

The terms “correlated” and “associated” are used interchangeably herein to refer to the association between two measurements (or measured entities). The disclosure provides genes, gene subsets, microRNAs, or microRNAs in combination with genes or gene subsets, the expression levels of which are associated with tumor stage. For example, the increased expression level of a gene or microRNA may be positively correlated (positively associated) with a good or positive prognosis. Such a positive correlation may be demonstrated statistically in various ways, e.g. by a cancer recurrence hazard ratio less than one. In another example, the increased expression level of a gene or microRNA may be negatively correlated (negatively associated) with a good or positive prognosis. In that case, for example, the patient may experience a cancer recurrence.

The terms “good prognosis” or “positive prognosis” as used herein refer to a beneficial clinical outcome, such as long-term survival without recurrence. The terms “bad prognosis” or “negative prognosis” as used herein refer to a negative clinical outcome, such as cancer recurrence.

The term “risk classification” means a grouping of subjects by the level of risk (or likelihood) that the subject will experience a particular clinical outcome. A subject may be classified into a risk group or classified at a level of risk based on the methods of the present disclosure, e.g. high, medium, or low risk. A “risk group” is a group of subjects or individuals with a similar level of risk for a particular clinical outcome.

The term “long-term” survival is used herein to refer to survival for a particular time period, e.g., for at least 5 years, or for at least 10 years.

The term “recurrence” is used herein to refer to local or distant recurrence (i.e., metastasis) of cancer. For example, prostate cancer can recur locally in the tissue next to the prostate or in the seminal vesicles. The cancer may also affect the surrounding lymph nodes in the pelvis or lymph nodes outside this area. Prostate cancer can also spread to tissues next to the prostate, such as pelvic muscles, bones, or other organs. Recurrence can be determined by clinical recurrence detected by, for example, imaging study or biopsy, or biochemical recurrence detected by, for example, sustained follow-up prostate-specific antigen (PSA) levels ≥0.4 ng/mL or the initiation of salvage therapy as a result of a rising PSA level.

The term “clinical recurrence-free interval (cRFI)” is used herein as time (in months) from surgery to first clinical recurrence or death due to clinical recurrence of prostate cancer. Losses due to incomplete follow-up, other primary cancers or death prior to clinical recurrence are considered censoring events; when these occur, the only information known is that up through the censoring time, clinical recurrence has not occurred in this subject. Biochemical recurrences are ignored for the purposes of calculating cRFI.

The term “biochemical recurrence-free interval (bRFI)” is used herein to mean the time (in months) from surgery to first biochemical recurrence of prostate cancer. Clinical recurrences, losses due to incomplete follow-up, other primary cancers, or death prior to biochemical recurrence are considered censoring events.

The term “Overall Survival (OS)” is used herein to refer to the time (in months) from surgery to death from any cause. Losses due to incomplete follow-up are considered censoring events. Biochemical recurrence and clinical recurrence are ignored for the purposes of calculating OS.

The term “Prostate Cancer-Specific Survival (PCSS)” is used herein to describe the time (in years) from surgery to death from prostate cancer. Losses due to incomplete follow-up or deaths from other causes are considered censoring events. Clinical recurrence and biochemical recurrence are ignored for the purposes of calculating PCSS.

The term “upgrading” or “upstaging” as used herein refers to a change in Gleason grade from 3+3 at the time of biopsy to 3+4 or greater at the time of radical prostatectomy (RP), or Gleason grade 3+4 at the time of biopsy to 4+3 or greater at the time of RP, or seminal vessical involvement (SVI), or extracapsular involvement (ECE) at the time of RP.

In practice, the calculation of the measures listed above may vary from study to study depending on the definition of events to be considered censored.

The term “microarray” refers to an ordered arrangement of hybridizable array elements, e.g. oligonucleotide or polynucleotide probes, on a substrate.

The term “polynucleotide” generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as defined herein include, without limitation, single- and double-stranded DNA, DNA including single- and double-stranded regions, single- and double-stranded RNA, and RNA including single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or include single- and double-stranded regions. In addition, the term “polynucleotide” as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. The term “polynucleotide” specifically includes cDNAs. The term includes DNAs (including cDNAs) and RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons, are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritiated bases, are included within the term “polynucleotides” as defined herein. In general, the term “polynucleotide” embraces all chemically, enzymatically and/or metabolically modified forms of unmodified polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells.

The term “oligonucleotide” refers to a relatively short polynucleotide, including, without limitation, single-stranded deoxyribonucleotides, single- or double-stranded ribonucleotides, RNArDNA hybrids and double-stranded DNAs. Oligonucleotides, such as single-stranded DNA probe oligonucleotides, are often synthesized by chemical methods, for example using automated oligonucleotide synthesizers that are commercially available. However, oligonucleotides can be made by a variety of other methods, including in vitro recombinant DNA-mediated techniques and by expression of DNAs in cells and organisms.

The term “Ct” as used herein refers to threshold cycle, the cycle number in quantitative polymerase chain reaction (qPCR) at which the fluorescence generated within a reaction well exceeds the defined threshold, i.e. the point during the reaction at which a sufficient number of amplicons have accumulated to meet the defined threshold.

The term “Cp” as used herein refers to “crossing point.” The Cp value is calculated by determining the second derivatives of entire qPCR amplification curves and their maximum value. The Cp value represents the cycle at which the increase of fluorescence is highest and where the logarithmic phase of a PCR begins.

The terms “threshold” or “thresholding” refer to a procedure used to account for non-linear relationships between gene expression measurements and clinical response as well as to further reduce variation in reported patient scores. When thresholding is applied, all measurements below or above a threshold are set to that threshold value. Non-linear relationship between gene expression and outcome could be examined using smoothers or cubic splines to model gene expression in Cox PH regression on recurrence free interval or logistic regression on recurrence status. D. Cox, Journal of the Royal Statistical Society, Series B 34:187-220 (1972). Variation in reported patient scores could be examined as a function of variability in gene expression at the limit of quantitation and/or detection for a particular gene.

As used herein, the term “amplicon,” refers to pieces of DNA that have been synthesized using amplification techniques, such as polymerase chain reactions (PCR) and ligase chain reactions.

“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology (Wiley Interscience Publishers, 1995).

“Stringent conditions” or “high stringency conditions”, as defined herein, typically: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide, followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-500 C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

The terms “splicing” and “RNA splicing” are used interchangeably and refer to RNA processing that removes introns and joins exons to produce mature mRNA with continuous coding sequence that moves into the cytoplasm of an eukaryotic cell.

The terms “co-express” and “co-expressed”, as used herein, refer to a statistical correlation between the amounts of different transcript sequences across a population of different patients. Pairwise co-expression may be calculated by various methods known in the art, e.g., by calculating Pearson correlation coefficients or Spearman correlation coefficients. Co-expressed gene cliques may also be identified using graph theory. An analysis of co-expression may be calculated using normalized expression data. A gene is said to be co-expressed with a particular disclosed gene when the expression level of the gene exhibits a Pearson correlation coefficient greater than or equal to 0.6.

A “computer-based system” refers to a system of hardware, software, and data storage medium used to analyze information. The minimum hardware of a patient computer-based system comprises a central processing unit (CPU), and hardware for data input, data output (e.g., display), and data storage. An ordinarily skilled artisan can readily appreciate that any currently available computer-based systems and/or components thereof are suitable for use in connection with the methods of the present disclosure. The data storage medium may comprise any manufacture comprising a recording of the present information as described above, or a memory access device that can access such a manufacture.

To “record” data, programming or other information on a computer readable medium refers to a process for storing information, using any such methods as known in the art. Any convenient data storage structure may be chosen, based on the means used to access the stored information. A variety of data processor programs and formats can be used for storage, e.g. word processing text file, database format, etc.

A “processor” or “computing means” references any hardware and/or software combination that will perform the functions required of it. For example, a suitable processor may be a programmable digital microprocessor such as available in the form of an electronic controller, mainframe, server or personal computer (desktop or portable). Where the processor is programmable, suitable programming can be communicated from a remote location to the processor, or previously saved in a computer program product (such as a portable or fixed computer readable storage medium, whether magnetic, optical or solid state device based). For example, a magnetic medium or optical disk may carry the programming, and can be read by a suitable reader communicating with each processor at its corresponding station.

As used herein, the terms “active surveillance” and “watchful waiting” mean closely monitoring a patient's condition without giving any treatment until symptoms appear or change. For example, in prostate cancer, watchful waiting is usually used in older men with other medical problems and early-stage disease.

As used herein, the term “surgery” applies to surgical methods undertaken for removal of cancerous tissue, including pelvic lymphadenectomy, radical prostatectomy, transurethral resection of the prostate (TURP), excision, dissection, and tumor biopsy/removal. The tumor tissue or sections used for gene expression analysis may have been obtained from any of these methods.

As used herein, the term “therapy” includes radiation, hormonal therapy, cryosurgery, chemotherapy, biologic therapy, and high-intensity focused ultrasound.

As used herein, the term “TMPRSS fusion” and “TMPRSS2 fusion” are used interchangeably and refer to a fusion of the androgen-driven TMPRSS2 gene with the ERG oncogene, which has been demonstrated to have a significant association with prostate cancer. S. Perner, et al., Urologe A. 46(7):754-760 (2007); S. A. Narod, et al., Br J Cancer 99(6):847-851 (2008). As used herein, positive TMPRSS fusion status indicates that the TMPRSS fusion is present in a tissue sample, whereas negative TMPRSS fusion status indicates that the TMPRSS fusion is not present in a tissue sample. Experts skilled in the art will recognize that there are numerous ways to determine TMPRSS fusion status, such as real-time, quantitative PCR or high-throughput sequencing. See, e.g., K. Mertz, et al., Neoplasis 9(3):200-206 (2007); C. Maher, Nature 458(7234):97-101 (2009).

Gene Expression Methods Using Genes, Gene Subsets, and Micrornas

The present disclosure provides molecular assays that involve measurement of expression level(s) of one or more genes, gene subsets, microRNAs, or one or more microRNAs in combination with one or more genes or gene subsets, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of cancer recurrence.

The present disclosure further provides methods to classify a prostate tumor based on expression level(s) of one or more genes and/or microRNAs. The disclosure further provides genes and/or microRNAs that are associated, positively or negatively, with a particular prognostic outcome. In exemplary embodiments, the clinical outcomes include cRFI and bRFI. In another embodiment, patients may be classified in risk groups based on the expression level(s) of one or more genes and/or microRNAs that are associated, positively or negatively, with a prognostic factor. In an exemplary embodiment, that prognostic factor is Gleason pattern.

Various technological approaches for determination of expression levels of the disclosed genes and microRNAs are set forth in this specification, including, without limitation, RT-PCR, microarrays, high-throughput sequencing, serial analysis of gene expression (SAGE) and Digital Gene Expression (DGE), which will be discussed in detail below. In particular aspects, the expression level of each gene or microRNA may be determined in relation to various features of the expression products of the gene including exons, introns, protein epitopes and protein activity.

The expression level(s) of one or more genes and/or microRNAs may be measured in tumor tissue. For example, the tumor tissue may obtained upon surgical removal or resection of the tumor, or by tumor biopsy. The tumor tissue may be or include histologically “normal” tissue, for example histologically “normal” tissue adjacent to a tumor. The expression level of genes and/or microRNAs may also be measured in tumor cells recovered from sites distant from the tumor, for example circulating tumor cells, body fluid (e.g., urine, blood, blood fraction, etc.).

The expression product that is assayed can be, for example, RNA or a polypeptide. The expression product may be fragmented. For example, the assay may use primers that are complementary to target sequences of an expression product and could thus measure full transcripts as well as those fragmented expression products containing the target sequence. Further information is provided in Table A (inserted in specification prior to claims).

The RNA expression product may be assayed directly or by detection of a cDNA product resulting from a PCR-based amplification method, e.g., quantitative reverse transcription polymerase chain reaction (qRT-PCR). (See e.g., U.S. Pat. No. 7,587,279). Polypeptide expression product may be assayed using immunohistochemistry (IHC). Further, both RNA and polypeptide expression products may also be is assayed using microarrays.

Clinical Utility

Prostate cancer is currently diagnosed using a digital rectal exam (DRE) and Prostate-specific antigen (PSA) test. If PSA results are high, patients will generally undergo a prostate tissue biopsy. The pathologist will review the biopsy samples to check for cancer cells and determine a Gleason score. Based on the Gleason score, PSA, clinical stage, and other factors, the physician must make a decision whether to monitor the patient, or treat the patient with surgery and therapy.

At present, clinical decision-making in early stage prostate cancer is governed by certain histopathologic and clinical factors. These include: (1) tumor factors, such as clinical stage (e.g. T1, T2), PSA level at presentation, and Gleason grade, that are very strong prognostic factors in determining outcome; and (2) host factors, such as age at diagnosis and co-morbidity. Because of these factors, the most clinically useful means of stratifying patients with localized disease according to prognosis has been through multifactorial staging, using the clinical stage, the serum PSA level, and tumor grade (Gleason grade) together. In the 2007 updated American Urological Association (AUA) guidelines for management of clinically localized prostate cancer, these parameters have been grouped to determine whether a patient is at low, intermediate, or high risk of biochemical (PSA) relapse after local therapy. I. Thompson, et al., Guideline for the management of clinically localized prostate cancer, J Urol. 177(6):2106-31 (2007).

Although such classifications have proven to be helpful in distinguishing patients with localized disease who may need adjuvant therapy after surgery/radiation, they have less ability to discriminate between indolent cancers, which do not need to be treated with local therapy, and aggressive tumors, which require local therapy. In fact, these algorithms are of increasingly limited use for deciding between conservative management and definitive therapy because the bulk of prostate cancers diagnosed in the PSA screening era now present with clinical stage T1c and PSA ≤10 ng/mL.

Patients with T1 prostate cancer have disease that is not clinically apparent but is discovered either at transurethral resection of the prostate (TURP, T1a, T1b) or at biopsy performed because of an elevated PSA (>4 ng/mL, T1c). Approximately 80% of the cases presenting in 2007 are clinical T1 at diagnosis. In a Scandinavian trial, OS at 10 years was 85% for patients with early stage prostate cancer (T1/T2) and Gleason score <7, after radical prostatectomy.

Patients with T2 prostate cancer have disease that is clinically evident and is organ confined; patients with T3 tumors have disease that has penetrated the prostatic capsule and/or has invaded the seminal vesicles. It is known from surgical series that clinical staging underestimates pathological stage, so that about 20% of patients who are clinically T2 will be pT3 after prostatectomy. Most of patients with T2 or T3 prostate cancer are treated with local therapy, either prostatectomy or radiation. The data from the Scandinavian trial suggest that for T2 patients with Gleason grade ≤7, the effect of prostatectomy on survival is at most 5% at 10 years; the majority of patients do not benefit from surgical treatment at the time of diagnosis. For T2 patients with Gleason >7 or for T3 patients, the treatment effect of prostatectomy is assumed to be significant but has not been determined in randomized trials. It is known that these patients have a significant risk (10-30%) of recurrence at 10 years after local treatment, however, there are no prospective randomized trials that define the optimal local treatment (radical prostatectomy, radiation) at diagnosis, which patients are likely to benefit from neo-adjuvant/adjuvant androgen deprivation therapy, and whether treatment (androgen deprivation, chemotherapy) at the time of biochemical failure (elevated PSA) has any clinical benefit.

Accurately determining Gleason scores from needle biopsies presents several technical challenges. First, interpreting histology that is “borderline” between Gleason pattern is highly subjective, even for urologic pathologists. Second, incomplete biopsy sampling is yet another reason why the “predicted” Gleason score on biopsy does not always correlate with the actual “observed” Gleason score of the prostate cancer in the gland itself. Hence, the accuracy of Gleason scoring is dependent upon not only the expertise of the pathologist reading the slides, but also on the completeness and adequacy of the prostate biopsy sampling strategy. T. Stamey, Urology 45:2-12 (1995). The gene/microRNA expression assay and associated information provided by the practice of the methods disclosed herein provide a molecular assay method to facilitate optimal treatment decision-making in early stage prostate cancer. An exemplary embodiment provides genes and microRNAs, the expression levels of which are associated (positively or negatively) with prostate cancer recurrence. For example, such a clinical tool would enable physicians to identify T2/T3 patients who are likely to recur following definitive therapy and need adjuvant treatment.

In addition, the methods disclosed herein may allow physicians to classify tumors, at a molecular level, based on expression level(s) of one or more genes and/or microRNAs that are significantly associated with prognostic factors, such as Gleason pattern and TMPRSS fusion status. These methods would not be impacted by the technical difficulties of intra-patient variability, histologically determining Gleason pattern in biopsy samples, or inclusion of histologically normal appearing tissue adjacent to tumor tissue. Multi-analyte gene/microRNA expression tests can be used to measure the expression level of one or more genes and/or microRNAs involved in each of several relevant physiologic processes or component cellular characteristics. The methods disclosed herein may group the genes and/or microRNAs. The grouping of genes and microRNAs may be performed at least in part based on knowledge of the contribution of those genes and/or microRNAs according to physiologic functions or component cellular characteristics, such as in the groups discussed above. Furthermore, one or more microRNAs may be combined with one or moregenes. The gene-microRNA combination may be selected based on the likelihood that the gene-microRNA combination functionally interact. The formation of groups (or gene subsets), in addition, can facilitate the mathematical weighting of the contribution of various expression levels to cancer recurrence. The weighting of a gene/microRNA group representing a physiological process or component cellular characteristic can reflect the contribution of that process or characteristic to the pathology of the cancer and clinical outcome.

Optionally, the methods disclosed may be used to classify patients by risk, for example risk of recurrence. Patients can be partitioned into subgroups (e.g., tertiles or quartiles) and the values chosen will define subgroups of patients with respectively greater or lesser risk.

The utility of a disclosed gene marker in predicting prognosis may not be unique to that marker. An alternative marker having an expression pattern that is parallel to that of a disclosed gene may be substituted for, or used in addition to, that co-expressed gene or microRNA. Due to the co-expression of such genes or microRNAs, substitution of expression level values should have little impact on the overall utility of the test. The closely similar expression patterns of two genes or microRNAs may result from involvement of both genes or microRNAs in the same process and/or being under common regulatory control in prostate tumor cells. The present disclosure thus contemplates the use of such co-expressed genes,gene subsets, or microRNAs as substitutes for, or in addition to, genes of the present disclosure.

Methods of Assaying Expression Levels of a Gene Product

The methods and compositions of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Exemplary techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, 2nd edition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology”, 4th edition (D. M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “Gene Transfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds., 1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987); and “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds., 1994).

Methods of gene expression profiling include methods based on hybridization analysis of polynucleotides, methods based on sequencing of polynucleotides, and proteomics-based methods. Exemplary methods known in the art for the quantification of RNA expression in a sample include northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283 (1999)); RNAse protection assays (Hod, Biotechniques 13:852-854 (1992)); and PCR-based methods, such as reverse transcription PCT (RT-PCR) (Weis et al., Trends in Genetics 8:263-264 (1992)). Antibodies may be employed that can recognize sequence-specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS).

Reverse Transcriptase PCR (RT-PCR)

Typically, mRNA or microRNA is isolated from a test sample. The starting material is typically total RNA isolated from a human tumor, usually from a primary tumor. Optionally, normal tissues from the same patient can be used as an internal control. Such normal tissue can be histologically-appearing normal tissue adjacent a tumor. mRNA or microRNA can be extracted from a tissue sample, e.g., from a sample that is fresh, frozen (e.g. fresh frozen), or paraffin-embedded and fixed (e.g. formalin-fixed).

General methods for mRNA and microRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker, Lab Invest. 56:A67 (1987), and De Andres et al., BioTechniques 18:42044 (1995). In particular, RNA isolation can be performed using a purification kit, buffer set and protease from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. For example, total RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MasterPureTM Complete DNA and RNA Purification Kit (EPICENTRE®, Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation.

The sample containing the RNA is then subjected to reverse transcription to produce cDNA from the RNA template, followed by exponential amplification in a PCR reaction. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit (Perkin Elmer, CA, USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction.

PCR-based methods use a thermostable DNA-dependent DNA polymerase, such as a Taq DNA polymerase. For example, TaqMan® PCR typically utilizes the 5′-nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5′ nuclease activity can be used. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction product. A third oligonucleotide, or probe, can be designed to facilitate detection of a nucleotide sequence of the amplicon located between the hybridization sites the two PCR primers. The probe can be detectably labeled, e.g., with a reporter dye, and can further be provided with both a fluorescent dye, and a quencher fluorescent dye, as in a Taqman® probe configuration. Where a Taqman® probe is used, during the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.

TaqMan® RT-PCR can be performed using commercially available equipment, such as, for example, high-throughput platforms such as the ABI PRISM 7700 Sequence Detection System® (Perkin-Elmer-Applied Biosystems, Foster City, Calif., USA), or Lightcycler (Roche Molecular Biochemicals, Mannheim, Germany). In a preferred embodiment, the procedure is run on a LightCycler® 480 (Roche Diagnostics) real-time PCR system, which is a microwell plate-based cycler platform.

5′-Nuclease assay data are commonly initially expressed as a threshold cycle (“CT”). Fluorescence values are recorded during every cycle and represent the amount of product amplified to that point in the amplification reaction. The threshold cycle (CT) is generally described as the point when the fluorescent signal is first recorded as statistically significant. Alternatively, data may be expressed as a crossing point (“Cp”). The Cp value is calculated by determining the second derivatives of entire qPCR amplification curves and their maximum value. The Cp value represents the cycle at which the increase of fluorescence is highest and where the logarithmic phase of a PCR begins.

To minimize errors and the effect of sample-to-sample variation, RT-PCR is usually performed using an internal standard. The ideal internal standard gene (also referred to as a reference gene) is expressed at a quite constant level among cancerous and non-cancerous tissue of the same origin (i.e., a level that is not significantly different among normal and cancerous tissues), and is not significantly affected by the experimental treatment (i.e., does not exhibit a significant difference in expression level in the relevant tissue as a result of exposure to chemotherapy), and expressed at a quite constant level among the same tissue taken from different patients. For example, reference genes useful in the methods disclosed herein should not exhibit significantly different expression levels in cancerous prostate as compared to normal prostate tissue. RNAs frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and β-actin. Exemplary reference genes used for normalization comprise one or more of the following genes: AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. Gene expression measurements can be normalized relative to the mean of one or more (e.g., 2, 3, 4, 5, or more) reference genes. Reference-normalized expression measurements can range from 2 to 15, where a one unit increase generally reflects a 2-fold increase in RNA quantity.

Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR. For further details see, e.g. Held et al., Genome Research 6:986-994 (1996).

The steps of a representative protocol for use in the methods of the present disclosure use fixed, paraffin-embedded tissues as the RNA source. For example, mRNA isolation, purification, primer extension and amplification can be performed according to methods available in the art. (see, e.g., Godfrey et al. J. Molec. Diagnostics 2: 84-91 (2000); Specht et al., Am. J. Pathol. 158: 419-29 (2001)). Briefly, a representative process starts with cutting about 10 μm thick sections of paraffin-embedded tumor tissue samples. The RNA is then extracted, and protein and DNA depleted from the RNA-containing sample. After analysis of the RNA concentration, RNA is reverse transcribed using gene specific primers followed by RT-PCR to provide for cDNA amplification products.

Design of Intron-Based PCR Primers and Probes

PCR primers and probes can be designed based upon exon or intron sequences present in the mRNA transcript of the gene of interest. Primer/probe design can be performed using publicly available software, such as the DNA BLAT software developed by Kent, W. J., Genome Res. 12(4):656-64 (2002), or by the BLAST software including its variations.

Where necessary or desired, repetitive sequences of the target sequence can be masked to mitigate non-specific signals. Exemplary tools to accomplish this include the Repeat Masker program available on-line through the Baylor College of Medicine, which screens DNA sequences against a library of repetitive elements and returns a query sequence in which the repetitive elements are masked. The masked intron sequences can then be used to design primer and probe sequences using any commercially or otherwise publicly available primer/probe design packages, such as Primer Express (Applied Biosystems); MGB assay-by-design (Applied Biosystems); Primer3 (Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. See S. Rrawetz, S. Misener, Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365-386 (Humana Press).

Other factors that can influence PCR primer design include primer length, melting temperature (Tm), and G/C content, specificity, complementary primer sequences, and 3′-end sequence. In general, optimal PCR primers are generally 17-30 bases in length, and contain about 20-80%, such as, for example, about 50-60% G+C bases, and exhibit Tm's between 50 and 80° C., e.g. about 50 to 70° C.

For further guidelines for PCR primer and probe design see, e.g. Dieffenbach, C W. et al, “General Concepts for PCR Primer Design” in: PCR Primer, A Laboratory Manual, Cold Spring Harbor Laboratory Press,. New York, 1995, pp. 133-155; Innis and Gelfand, “Optimization of PCRs” in: PCR Protocols, A Guide to Methods and Applications, CRC Press, London, 1994, pp. 5-11; and Plasterer, T. N. Primerselect: Primer and probe design. Methods Mol. Biol. 70:520-527 (1997), the entire disclosures of which are hereby expressly incorporated by reference.

Table A provides further information concerning the primer, probe, and amplicon sequences associated with the Examples disclosed herein.

MassARRAY® System

In MassARRAY-based methods, such as the exemplary method developed by Sequenom, Inc. (San Diego, Calif.) following the isolation of RNA and reverse transcription, the obtained cDNA is spiked with a synthetic DNA molecule (competitor), which matches the targeted cDNA region in all positions, except a single base, and serves as an internal standard. The cDNA/competitor mixture is PCR amplified and is subjected to a post-PCR shrimp alkaline phosphatase (SAP) enzyme treatment, which results in the dephosphorylation of the remaining nucleotides. After inactivarion of the alkaline phosphatase, the PCR products from the competitor and cDNA are subjected to primer extension, which generates distinct mass signals for the competitor- and cDNA-derives PCR products. After purification, these products are dispensed on a chip array, which is pre-loaded with components needed for analysis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The cDNA present in the reaction is then quantified by analyzing the ratios of the peak areas in the mass spectrum generated. For further details see, e.g. Ding and Cantor, Proc. Natl. Acad. Sci. USA 100:3059-3064 (2003).

Other PCR-Based Methods

Further PCR-based techniques that can find use in the methods disclosed herein include, for example, BeadArray® technology (Illumina, San Diego, Calif.; Oliphant et al., Discovery of Markers for Disease (Supplement to Biotechniques), June 2002; Ferguson et al., Analytical Chemistry 72:5618 (2000)); BeadsArray for Detection of Gene Expression® (BADGE), using the commercially available LuminexlOO LabMAP® system and multiple color-coded microspheres (Luminex Corp., Austin, Tex.) in a rapid assay for gene expression (Yang et al., Genome Res. 11:1888-1898 (2001)); and high coverage expression profiling (HiCEP) analysis (Fukumura et al., Nucl. Acids. Res. 31(16) e94 (2003).

Microarrays

Expression levels of a gene or microArray of interest can also be assessed using the microarray technique. In this method, polynucleotide sequences of interest (including cDNAs and oligonucleotides) are arrayed on a substrate. The arrayed sequences are then contacted under conditions suitable for specific hybridization with detectably labeled cDNA generated from RNA of a test sample. As in the RT-PCR method, the source of RNA typically is total RNA isolated from a tumor sample, and optionally from normal tissue of the same patient as an internal control or cell lines. RNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples.

For example, PCR amplified inserts of cDNA clones of a gene to be assayed are applied to a substrate in a dense array. Usually at least 10,000 nucleotide sequences are applied to the substrate. For example, the microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions. Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array. After washing under stringent conditions to remove non-specifically bound probes, the chip is scanned by confocal laser microscopy or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding RNA abundance.

With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pair wise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. The miniaturized scale of the hybridization affords a convenient and rapid evaluation of the expression pattern for large numbers of genes. Such methods have been shown to have the sensitivity required to detect rare transcripts, which are expressed at a few copies per cell, and to reproducibly detect at least approximately two-fold differences in the expression levels (Schena et at, Proc. Natl. Acad. ScL USA 93(2):106-149 (1996)). Microarray analysis can be performed by commercially available equipment, following manufacturer's protocols, such as by using the Affymetrix GenChip® technology, or Incyte's microarray technology.

Serial Analysis of Gene Expression (SAGE)

Serial analysis of gene expression (SAGE) is a method that allows the simultaneous and quantitative analysis of a large number of gene transcripts, without the need of providing an individual hybridization probe for each transcript. First, a short sequence tag (about 10-14 bp) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript. Then, many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously. The expression pattern of any population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag. For more details see, e.g. Velculescu et al., Science 270:484-487 (1995); and Velculescu et al., Cell 88:243-51 (1997).

Gene Expression Analysis by Nucleic Acid Sequencing

Nucleic acid sequencing technologies are suitable methods for analysis of gene expression. The principle underlying these methods is that the number of times a cDNA sequence is detected in a sample is directly related to the relative expression of the RNA corresponding to that sequence. These methods are sometimes referred to by the term Digital Gene Expression (DGE) to reflect the discrete numeric property of the resulting data. Early methods applying this principle were Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS). See, e.g., S. Brenner, et al., Nature Biotechnology 18(6):630-634 (2000). More recently, the advent of “next-generation” sequencing technologies has made DGE simpler, higher throughput, and more affordable. As a result, more laboratories are able to utilize DGE to screen the expression of more genes in more individual patient samples than previously possible. See, e.g., J. Marioni, Genome Research 18(9):1509-1517 (2008); R. Morin, Genome Research 18(4):610-621 (2008); A. Mortazavi, Nature Methods 5(7):621-628 (2008); N. Cloonan, Nature Methods 5(7):613-619 (2008).

Isolating RNA from Body Fluids

Methods of isolating RNA for expression analysis from blood, plasma and serum (see, e.g., K. Enders, et al., Clin Chem 48,1647-53 (2002) (and references cited therein) and from urine (see, e.g., R. Boom, et al., J Clin Microbiol. 28, 495-503 (1990) and references cited therein) have been described.

Immunohistochemistry

Immunohistochemistry methods are also suitable for detecting the expression levels of genes and applied to the method disclosed herein. Antibodies (e.g., monoclonal antibodies) that specifically bind a gene product of a gene of interest can be used in such methods. The antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten' labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibody can be used in conjunction with a labeled secondary antibody specific for the primary antibody. Immunohistochemistry protocols and kits are well known in the art and are commercially available.

Proteomics

The term “proteome” is defined as the totality of the proteins present in a sample (e.g. tissue, organism, or cell culture) at a certain point of time. Proteomics includes, among other things, study of the global changes of protein expression in a sample (also referred to as “expression proteomics”). Proteomics typically includes the following steps: (1) separation of individual proteins in a sample by 2-D gel electrophoresis (2-D PAGE); (2) identification of the individual proteins recovered from the gel, e.g. my mass spectrometry or N-terminal sequencing, and (3) analysis of the data using bioinformatics.

General Description of the mRNA/microRNA Isolation, Purification and Amplification

The steps of a representative protocol for profiling gene expression using fixed, paraffin-embedded tissues as the RNA source, including mRNA or microRNA isolation, purification, primer extension and amplification are provided in various published journal articles. (See, e.g., T. E. Godfrey, et al,. J. Molec. Diagnostics 2: 84-91 (2000); K. Specht et al., Am. J. Pathol. 158: 419-29 (2001), M. Cronin, et al., Am J Pathol 164:35-42 (2004)). Briefly, a representative process starts with cutting a tissue sample section (e.g.about 10 μm thick sections of a paraffin-embedded tumor tissue sample). The RNA is then extracted, and protein and DNA are removed. After analysis of the RNA concentration, RNA repair is performed if desired. The sample can then be subjected to analysis, e.g., by reverse transcribed using gene specific promoters followed by RT-PCR.

Statistical Analysis of Expression Levels in Identification of Genes and MicroRNAs

One skilled in the art will recognize that there are many statistical methods that may be used to determine whether there is a significant relationship between a parameter of interest (e.g., recurrence) and expression levels of a marker gene/microRNA as described here. In an exemplary embodiment, the present invention provides a stratified cohort sampling design (a form of case-control sampling) using tissue and data from prostate cancer patients. Selection of specimens was stratified by T stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason Score (low/intermediate, high). All patients with clinical recurrence were selected and a sample of patients who did not experience a clinical recurrence was selected. For each patient, up to two enriched tumor specimens and one normal-appearing tissue sample was assayed.

All hypothesis tests were reported using two-sided p-values. To investigate if there is a significant relationship of outcomes (clinical recurrence-free interval (cRFI), biochemical recurrence-free interval (bRFI), prostate cancer-specific survival (PCSS), and overall survival (OS)) with individual genes and/or microRNAs, demographic or clinical covariates Cox Proportional Hazards (PH) models using maximum weighted pseudo partial-likelihood estimators were used and p-values from Wald tests of the null hypothesis that the hazard ratio (HR) is one are reported. To investigate if there is a significant relationship between individual genes and/or microRNAs and Gleason pattern of a particular sample, ordinal logistic regression models using maximum weighted likelihood methods were used and p-values from Wald tests of the null hypothesis that the odds ratio (OR) is one are reported.

Coexpression Analysis

The present disclosure provides a method to determine tumor stage based on the expression of staging genes, or genes that co-express with particular staging genes. To perform particular biological processes, genes often work together in a concerted way, i.e. they are co-expressed. Co-expressed gene groups identified for a disease process like cancer can serve as biomarkers for tumor status and disease progression. Such co-expressed genes can be assayed in lieu of, or in addition to, assaying of the staging gene with which they are co-expressed.

In an exemplary embodiment, the joint correlation of gene expression levels among prostate cancer specimens under study may be assessed. For this purpose, the correlation structures among genes and specimens may be examined through hierarchical cluster methods. This information may be used to confirm that genes that are known to be highly correlated in prostate cancer specimens cluster together as expected. Only genes exhibiting a nominally significant (unadjusted p<0.05) relationship with cRFI in the univariate Cox PH regression analysis will be included in these analyses.

One skilled in the art will recognize that many co-expression analysis methods now known or later developed will fall within the scope and spirit of the present invention. These methods may incorporate, for example, correlation coefficients, co-expression network analysis, clique analysis, etc., and may be based on expression data from RT-PCR, microarrays, sequencing, and other similar technologies. For example, gene expression clusters can be identified using pair-wise analysis of correlation based on Pearson or Spearman correlation coefficients. (See, e.g., Pearson K. and Lee A., Biometrika 2, 357 (1902); C. Spearman, Amer. J. Psychol 15:72-101 (1904); J. Myers, A. Well, Research Design and Statistical Analysis, p. 508 (2nd Ed., 2003).)

Normalization of Expression Levels

The expression data used in the methods disclosed herein can be normalized. Normalization refers to a process to correct for (normalize away), for example, differences in the amount of RNA assayed and variability in the quality of the RNA used, to remove unwanted sources of systematic variation in Ct or Cp measurements, and the like. With respect to RT-PCR experiments involving archived fixed paraffin embedded tissue samples, sources of systematic variation are known to include the degree of RNA degradation relative to the age of the patient sample and the type of fixative used to store the sample. Other sources of systematic variation are attributable to laboratory processing conditions.

Assays can provide for normalization by incorporating the expression of certain normalizing genes, which do not significantly differ in expression levels under the relevant conditions. Exemplary normalization genes disclosed herein include housekeeping genes. (See, e.g., E. Eisenberg, et al., Trends in Genetics 19(7):362-365 (2003).) Normalization can be based on the mean or median signal (Ct or Cp) of all of the assayed genes or a large subset thereof (global normalization approach). In general, the normalizing genes, also referred to as reference genes should be genes that are known not to exhibit significantly different expression in prostate cancer as compared to non-cancerous prostate tissue, and are not significantly affected by various sample and process conditions, thus provide for normalizing away extraneous effects.

In exemplary embodiments, one or more of the following genes are used as references by which the mRNA or microRNA expression data is normalized: AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. In another exemplary embodiment, one or more of the following microRNAs are used as references by which the expression data of microRNAs are normalized: hsa-miR-106a; hsa-miR-146b-5p; hsa-miR-191; hsa-miR-19b; and hsa-miR-92a. The calibrated weighted average CT or Cp measurements for each of the prognostic and predictive genes or microRNAs may be normalized relative to the mean of five or more reference genes or microRNAs.

Those skilled in the art will recognize that normalization may be achieved in numerous ways, and the techniques described above are intended only to be exemplary, not exhaustive.

Standardization of Expression Levels

The expression data used in the methods disclosed herein can be standardized. Standardization refers to a process to effectively put all the genes or microRNAs on a comparable scale. This is performed because some genes or microRNAs will exhibit more variation (a broader range of expression) than others. Standardization is performed by dividing each expression value by its standard deviation across all samples for that gene or microRNA. Hazard ratios are then interpreted as the relative risk of recurrence per 1 standard deviation increase in expression.

Kits of the Invention

The materials for use in the methods of the present invention are suited for preparation of kits produced in accordance with well-known procedures. The present disclosure thus provides kits comprising agents, which may include gene (or microRNA)-specific or gene (or microRNA)-selective probes and/or primers, for quantifying the expression of the disclosed genes or microRNAs for predicting prognostic outcome or response to treatment. Such kits may optionally contain reagents for the extraction of RNA from tumor samples, in particular fixed paraffin-embedded tissue samples and/or reagents for RNA amplification. In addition, the kits may optionally comprise the reagent(s) with an identifying description or label or instructions relating to their use in the methods of the present invention. The kits may comprise containers (including microliter plates suitable for use in an automated implementation of the method), each with one or more of the various materials or reagents (typically in concentrated form) utilized in the methods, including, for example, chromatographic columns, pre-fabricated microarrays, buffers, the appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP and dTTP; or rATP, rCTP, rGTP and UTP), reverse transcriptase, DNA polymerase, RNA polymerase, and one or more probes and primers of the present invention (e.g., appropriate length poly(T) or random primers linked to a promoter reactive with the RNA polymerase). Mathematical algorithms used to estimate or quantify prognostic or predictive information are also properly potential components of kits.

Reports

The methods of this invention, when practiced for commercial diagnostic purposes, generally produce a report or summary of information obtained from the herein-described methods. For example, a report may include information concerning expression levels of one or more genes and /or microRNAs, classification of the tumor or the patient's risk of recurrence, the patient's likely prognosis or risk classification, clinical and pathologic factors, and/or other information. The methods and reports of this invention can further include storing the report in a database. The method can create a record in a database for the subject and populate the record with data. The report may be a paper report, an auditory report, or an electronic record. The report may be displayed and/or stored on a computing device (e.g., handheld device, desktop computer, smart device, website, etc.). It is contemplated that the report is provided to a physician and/or the patient. The receiving of the report can further include establishing a network connection to a server computer that includes the data and report and requesting the data and report from the server computer.

Computer Program

The values from the assays described above, such as expression data, can be calculated and stored manually. Alternatively, the above-described steps can be completely or partially performed by a computer program product. The present invention thus provides a computer program product including a computer readable storage medium having a computer program stored on it. The program can, when read by a computer, execute relevant calculations based on values obtained from analysis of one or more biological sample from an individual (e.g., gene expression levels, normalization, standardization, thresholding, and conversion of values from assays to a score and/or text or graphical depiction of tumor stage and related information). The computer program product has stored therein a computer program for performing the calculation.

The present disclosure provides systems for executing the program described above, which system generally includes: a) a central computing environment; b) an input device, operatively connected to the computing environment, to receive patient data, wherein the patient data can include, for example, expression level or other value obtained from an assay using a biological sample from the patient, or microarray data, as described in detail above; c) an output device, connected to the computing environment, to provide information to a user (e.g., medical personnel); and d) an algorithm executed by the central computing environment (e.g., a processor), where the algorithm is executed based on the data received by the input device, and wherein the algorithm calculates an expression score, thresholding, or other functions described herein. The methods provided by the present invention may also be automated in whole or in part.

All aspects of the present invention may also be practiced such that a limited number of additional genes and/or microRNAs that are co-expressed or functionally related with the disclosed genes, for example as evidenced by statistically meaningful Pearson and/or Spearman correlation coefficients, are included in a test in addition to and/or in place of disclosed genes.

Having described the invention, the same will be more readily understood through reference to the following Examples, which are provided by way of illustration, and are not intended to limit the invention in any way.

EXAMPLES Example 1 RNA Yield and Gene Expression Profiles in Prostate Cancer Biopsy Cores

Clinical tools based on prostate needle core biopsies are needed to guide treatment planning at diagnosis for men with localized prostate cancer. Limiting tissue in needle core biopsy specimens poses significant challenges to the development of molecular diagnostic tests. This study examined RNA extraction yields and gene expression profiles using an RT-PCR assay to characterize RNA from manually micro-dissected fixed paraffin embedded (FPE) prostate cancer needle biopsy cores. It also investigated the association of RNA yields and gene expression profiles with Gleason score in these specimens.

Patients and Samples

This study determined the feasibility of gene expression profile analysis in prostate cancer needle core biopsies by evaluating the quantity and quality of RNA extracted from fixed paraffin-embedded (FPE) prostate cancer needle core biopsy specimens. Forty-eight (48) formalin-fixed blocks from prostate needle core biopsy specimens were used for this study. Classification of specimens was based on interpretation of the Gleason score (2005 Int'l Society of Urological Pathology Consensus Conference) and percentage tumor (<33%, 33-66%, >66%) involvement as assessed by pathologists.

TABLE 1 Distribution of cases Gleason score ~<33% ~33-66% ~>66% Category Tumor Tumor Tumor Low (≤6)  5  5  6 Intermediate (7)  5  5  6 High (8, 9, 10)  5  5  6 Total 15 15 18

Assay Methods

Fourteen (14) serial 5 μm unstained sections from each FPE tissue block were included in the study. The first and last sections for each case were H&E stained and histologically reviewed to confirm the presence of tumor and for tumor enrichment by manual micro-dissection.

RNA from enriched tumor samples was extracted using a manual RNA extraction process. RNA was quantitated using the RiboGreen® assay and tested for the presence of genomic DNA contamination. Samples with sufficient RNA yield and free of genomic DNA tested for gene expression levels of a 24-gene panel of reference and cancer-related genes using quantitative RT-PCR. The expression was normalized to the average of 6 reference genes (AAMP, ARF1, ATP5E, CLTC, EEF1A1, and GPX1).

Statistical Methods

Descriptive statistics and graphical displays were used to summarize standard pathology metrics and gene expression, with stratification for Gleason Score category and percentage tumor involvement category. Ordinal logistic regression was used to evaluate the relationship between gene expression and Gleason Score category.

Results

The RNA yield per unit surface area ranged from 16 to 2406 ng/mm2. Higher RNA yield was observed in samples with higher percent tumor involvement (p=0.02) and higher Gleason score (p=0.01). RNA yield was sufficient (>200 ng) in 71% of cases to permit 96-well RT-PCR, with 87% of cases having >100 ng RNA yield. The study confirmed that gene expression from prostate biopsies, as measured by qRT-PCR, was comparable to FPET samples used in commercial molecular assays for breast cancer. In addition, it was observed that greater biopsy RNA yields are found with higher Gleason score and higher percent tumor involvement. Nine genes were identified as significantly associated with Gleason score (p<0.05) and there was a large dynamic range observed for many test genes.

Example 2 Gene Expression Analysis for Genes Associated with Prognosis in Prostate Cancer

Patients and Samples

Approximately 2600 patients with clinical stage T1/T2 prostate cancer treated with radical prostatectomy (RP) at the Cleveland Clinic between 1987 and 2004 were identified. Patients were excluded from the study design if they received neo-adjuvant and/or adjuvant therapy, if pre-surgical PSA levels were missing, or if no tumor block was available from initial diagnosis. 127 patients with clinical recurrence and 374 patients without clinical recurrence after radical prostatectomy were randomly selected using a cohort sampling design. The specimens were stratified by T stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason score (low/intermediate, high). Of the 501 sampled patients, 51 were excluded for insufficient tumor; 7 were excluded due to clinical ineligibility; 2 were excluded due to poor quality of gene expression data; and 10 were excluded because primary Gleason pattern was unavailable. Thus, this gene expression study included tissue and data from 111 patients with clinical recurrence and 330 patients without clinical recurrence after radical prostatectomies performed between 1987 and 2004 for treatment of early stage (T1, T2) prostate cancer.

Two fixed paraffin embedded (FPE) tissue specimens were obtained from prostate tumor specimens in each patient. The sampling method (sampling method A or B) depended on whether the highest Gleason pattern is also the primary Gleason pattern. For each specimen selected, the invasive cancer cells were at least 5.0 mm in dimension, except in the instances of pattern 5, where 2.2 mm was accepted. Specimens were spatially distinct where possible.

TABLE 2 Sampling Methods Sampling Method A Sampling Method B For patients whose prostatectomy primary For patients whose prostatectomy primary Gleason pattern is also the highest Gleason Gleason pattern is not the highest Gleason pattern pattern Specimen 1 (A1) = primary Gleason pattern Specimen 1 (B1) = highest Gleason pattern Select and mark largest focus (greatest cross- Select highest Gleason pattern tissue from sectional area) of primary Gleason pattern spatially distinct area from specimen B2, if tissue. Invasive cancer area ≥ 5.0 mm. possible. Invasive cancer area at least 5.0 mm if selecting secondary pattern, at least 2.2 mm if selecting Gleason pattern 5. Specimen 2 (A2) = secondary Gleason pattern Specimen 2 (B2) = primary Gleason pattern Select and mark secondary Gleason pattern Select largest focus (greatest cross-sectional tissue from spatially distinct area from area) of primary Gleason pattern tissue. specimen A1. Invasive cancer area ≥ 5.0 mm. Invasive cancer area ≥ 5.0 mm.

Histologically normal appearing tissue (NAT) adjacent to the tumor specimen (also referred to in these Examples as “non-tumor tissue”) was also evaluated. Adjacent tissue was collected 3 mm from the tumor to 3 mm from the edge of the FPET block. NAT was preferentially sampled adjacent to the primary Gleason pattern. In cases where there was insufficient NAT adjacent to the primary Gleason pattern, then NAT was sampled adjacent to the secondary or highest Gleason pattern (A2 or B1) per the method set forth in Table 2. Six (6) 10 μm sections with beginning H&E at 5 μm and ending unstained slide at 5 μm were prepared from each fixed paraffin-embedded tumor (FPET) block included in the study. All cases were histologically reviewed and manually micro-dissected to yield two enriched tumor samples and, where possible, one normal tissue sample adjacent to the tumor specimen.

Assay Method

In this study, RT-PCR analysis was used to determine RNA expression levels for 738 genes and chromosomal rearrangements (e.g., TMPRSS2-ERG fusion or other ETS family genes) in prostate cancer tissue and surrounding NAT in patients with early-stage prostate cancer treated with radical prostatectomy.

The samples were quantified using the RiboGreen assay and a subset tested for presence of genomic DNA contamination. Samples were taken into reverse transcription (RT) and quantitative polymerase chain reaction (qPCR). All analyses were conducted on reference-normalized gene expression levels using the average of the of replicate well crossing point (CP) values for the 6 reference genes (AAMP, ARF1, ATP5E, CLTC, GPS1, PGK1).

Statistical Analysis and Results

Primary statistical analyses involved 111 patients with clinical recurrence and 330 patients without clinical recurrence after radical prostatectomy for early-stage prostate cancer stratified by T-stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy Gleason score (low/intermediate, high). Gleason score categories are defined as follows: low (Gleason score≤6), intermediate (Gleason score=7), and high (Gleason score≥8). A patient was included in a specified analysis if at least one sample for that patient was evaluable. Unless otherwise stated, all hypothesis tests were reported using two-sided p-values. The method of Storey was applied to the resulting set of p-values to control the false discovery rate (FDR) at 20%. J. Storey, R. Tibshirani, Estimating the Positive False Discovery Rate Under Dependence, with Applications to DNA Microarrays, Dept. of Statistics, Stanford Univ. (2001).

Analysis of gene expression and recurrence-free interval was based on univariate Cox Proportional Hazards (PH) models using maximum weighted pseudo-partial-likelihood estimators for each evaluable gene in the gene list (727 test genes and 5 reference genes). P-values were generated using Wald tests of the null hypothesis that the hazard ratio (HR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values <0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2).

Analysis of gene expression and Gleason pattern (3, 4, 5) was based on univariate ordinal logistic regression models using weighted maximum likelihood estimators for each gene in the gene list (727 test genes and 5 reference genes). P-values were generated using a Wald test of the null hypothesis that the odds ratio (OR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values<0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2).

It was determined whether there is a significant relationship between cRFI and selected demographic, clinical, and pathology variables, including age, race, clinical tumor stage, pathologic tumor stage, location of selected tumor specimens within the prostate (peripheral versus transitional zone), PSA at the time of surgery, overall Gleason score from the radical prostatectomy, year of surgery, and specimen Gleason pattern. Separately for each demographic or clinical variable, the relationship between the clinical covariate and cRFI was modeled using univariate Cox PH regression using weighted pseudo partial-likelihood estimators and a p-value was generated using Wald's test of the null hypothesis that the hazard ratio (HR) is one. Covariates with unadjusted p-values<0.2 may have been included in the covariate-adjusted analyses.

It was determined whether there was a significant relationship between each of the individual cancer-related genes and cRFI after controlling for important demographic and clinical covariates. Separately for each gene, the relationship between gene expression and cRFI was modeled using multivariate Cox PH regression using weighted pseudo partial-likelihood estimators including important demographic and clinical variables as covariates. The independent contribution of gene expression to the prediction of cRFI was tested by generating a p-value from a Wald test using a model that included clinical covariates for each nodule (specimens as defined in Table 2). Un-adjusted p-values<0.05 were considered statistically significant.

Tables 3A and 3B provide genes significantly associated (p<0.05), positively or negatively, with Gleason pattern in the primary and/or highest Gleason pattern. Increased expression of genes in Table 3A is positively associated with higher Gleason score, while increased expression of genes in Table 3B are negatively associated with higher Gleason score.

TABLE 3A Gene significantly (p < 0.05) associated with Gleason pattern for all specimens in the primary Gleason pattern or highest Gleason pattern odds ratio (OR) > 1.0 (Increased expression is positively associated with higher Gleason Score) Table 3A Primary Pattern Highest Pattern Official Symbol OR p-value OR p-value ALCAM 1.73 <.001 1.36 0.009 ANLN 1.35 0.027 APOC1 1.47 0.005 1.61 <.001 APOE 1.87 <.001 2.15 <.001 ASAP2 1.53 0.005 ASPN 2.62 <.001 2.13 <.001 ATP5E 1.35 0.035 AURKA 1.44 0.010 AURKB 1.59 <.001 1.56 <.001 BAX 1.43 0.006 BGN 2.58 <.001 2.82 <.001 BIRC5 1.45 0.003 1.79 <.001 BMP6 2.37 <.001 1.68 <.001 BMPR1B 1.58 0.002 BRCA2 1.45 0.013 BUB1 1.73 <.001 1.57 <.001 CACNA1D 1.31 0.045 1.31 0.033 CADPS 1.30 0.023 CCNB1 1.43 0.023 CCNE2 1.52 0.003 1.32 0.035 CD276 2.20 <.001 1.83 <.001 CD68 1.36 0.022 CDC20 1.69 <.001 1.95 <.001 CDC6 1.38 0.024 1.46 <.001 CDH11 1.30 0.029 CDKN2B 1.55 0.001 1.33 0.023 CDKN2C 1.62 <.001 1.52 <.001 CDKN3 1.39 0.010 1.50 0.002 CENPF 1.96 <.001 1.71 <.001 CHRAC1 1.34 0.022 CLDN3 1.37 0.029 COL1A1 2.23 <.001 2.22 <.001 COL1A2 1.42 0.005 COL3A1 1.90 <.001 2.13 <.001 COL8A1 1.88 <.001 2.35 <.001 CRISP3 1.33 0.040 1.26 0.050 CTHRC1 2.01 <.001 1.61 <.001 CTNND2 1.48 0.007 1.37 0.011 DAPK1 1.44 0.014 DIAPH1 1.34 0.032 1.79 <.001 DIO2 1.56 0.001 DLL4 1.38 0.026 1.53 <.001 ECE1 1.54 0.012 1.40 0.012 ENY2 1.35 0.046 1.35 0.012 EZH2 1.39 0.040 F2R 2.37 <.001 2.60 <.001 FAM49B 1.57 0.002 1.33 0.025 FAP 2.36 <.001 1.89 <.001 FCGR3A 2.10 <.001 1.83 <.001 GNPTAB 1.78 <.001 1.54 <.001 GSK3B 1.39 0.018 HRAS 1.62 0.003 HSD17B4 2.91 <.001 1.57 <.001 HSPA8 1.48 0.012 1.34 0.023 IFI30 1.64 <.001 1.45 0.013 IGFBP3 1.29 0.037 IL11 1.52 0.001 1.31 0.036 INHBA 2.55 <.001 2.30 <.001 ITGA4 1.35 0.028 JAG1 1.68 <.001 1.40 0.005 KCNN2 1.50 0.004 KCTD12 1.38 0.012 KHDRBS3 1.85 <.001 1.72 <.001 KIF4A 1.50 0.010 1.50 <.001 KLK14 1.49 0.001 1.35 <.001 KPNA2 1.68 0.004 1.65 0.001 KRT2 1.33 0.022 KRT75 1.27 0.028 LAMC1 1.44 0.029 LAPTM5 1.36 0.025 1.31 0.042 LTBP2 1.42 0.023 1.66 <.001 MANF 1.34 0.019 MAOA 1.55 0.003 1.50 <.001 MAP3K5 1.55 0.006 1.44 0.001 MDK 1.47 0.013 1.29 0.041 MDM2 1.31 0.026 MELK 1.64 <.001 1.64 <.001 MMP11 2.33 <.001 1.66 <.001 MYBL2 1.41 0.007 1.54 <.001 MYO6 1.32 0.017 NETO2 1.36 0.018 NOX4 1.84 <.001 1.73 <.001 NPM1 1.68 0.001 NRIP3 1.36 0.009 NRP1 1.80 0.001 1.36 0.019 OSM 1.33 0.046 PATE1 1.38 0.032 PECAM1 1.38 0.021 1.31 0.035 PGD 1.56 0.010 PLK1 1.51 0.004 1.49 0.002 PLOD2 1.29 0.027 POSTN 1.70 0.047 1.55 0.006 PPP3CA 1.38 0.037 1.37 0.006 PTK6 1.45 0.007 1.53 <.001 PTTG1 1.51 <.001 RAB31 1.31 0.030 RAD21 2.05 <.001 1.38 0.020 RAD51 1.46 0.002 1.26 0.035 RAF1 1.46 0.017 RALBP1 1.37 0.043 RHOC 1.33 0.021 ROBO2 1.52 0.003 1.41 0.006 RRM2 1.77 <.001 1.50 <.001 SAT1 1.67 0.002 1.61 <.001 SDC1 1.66 0.001 1.46 0.014 SEC14L1 1.53 0.003 1.62 <.001 SESN3 1.76 <.001 1.45 <.001 SFRP4 2.69 <.001 2.03 <.001 SHMT2 1.69 0.007 1.45 0.003 SKIL 1.46 0.005 SOX4 1.42 0.016 1.27 0.031 SPARC 1.40 0.024 1.55 <.001 SPINK1 1.29 0.002 SPP1 1.51 0.002 1.80 <.001 TFDP1 1.48 0.014 THBS2 1.87 <.001 1.65 <.001 THY1 1.58 0.003 1.64 <.001 TK1 1.79 <.001 1.42 0.001 TOP2A 2.30 <.001 2.01 <.001 TPD52 1.95 <.001 1.30 0.037 TPX2 2.12 <.001 1.86 <.001 TYMP 1.36 0.020 TYMS 1.39 0.012 1.31 0.036 UBE2C 1.66 <.001 1.65 <.001 UBE2T 1.59 <.001 1.33 0.017 UGDH 1.28 0.049 UGT2B15 1.46 0.001 1.25 0.045 UHRF1 1.95 <.001 1.62 <.001 VDR 1.43 0.010 1.39 0.018 WNT5A 1.54 0.001 1.44 0.013

TABLE 3B Gene significantly (p < 0.05) associated with Gleason pattern for all specimens in the primary Gleason pattern or highest Gleason pattern odds ratio (OR) <1.0 (Increased expression is negatively associated with higher Gleason score) Table 3B Primary Pattern Highest Pattern Official Symbol OR p-value OR p-value ABCA5 0.78 0.041 ABCG2 0.65 0.001 0.72 0.012 ACOX2 0.44 <.001 0.53 <.001 ADH5 0.45 <.001 0.42 <.001 AFAP1 0.79 0.038 AIG1 0.77 0.024 AKAP1 0.63 0.002 AKR1C1 0.66 0.003 0.63 <.001 AKT3 0.68 0.006 0.77 0.010 ALDH1A2 0.28 <.001 0.33 <.001 ALKBH3 0.77 0.040 0.77 0.029 AMPD3 0.67 0.007 ANPEP 0.68 0.008 0.59 <.001 ANXA2 0.72 0.018 APC 0.69 0.002 AXIN2 0.46 <.001 0.54 <.001 AZGP1 0.52 <.001 0.53 <.001 BIK 0.69 0.006 0.73 0.003 BIN1 0.43 <.001 0.61 <.001 BTG3 0.79 0.030 BTRC 0.48 <.001 0.62 <.001 C7 0.37 <.001 0.55 <.001 CADM1 0.56 <.001 0.69 0.001 CAV1 0.58 0.002 0.70 0.009 CAV2 0.65 0.029 CCNH 0.67 0.006 0.77 0.048 CD164 0.59 0.003 0.57 <.001 CDC25B 0.77 0.035 CDH1 0.66 <.001 CDK2 0.71 0.003 CDKN1C 0.58 <.001 0.57 <.001 CDS2 0.69 0.002 CHN1 0.66 0.002 COL6A1 0.44 <.001 0.66 <.001 COL6A3 0.66 0.006 CSRP1 0.42 0.006 CTGF 0.74 0.043 CTNNA1 0.70 <.001 0.83 0.018 CTNNB1 0.70 0.019 CTNND1 0.75 0.028 CUL1 0.74 0.011 CXCL12 0.54 <.001 0.74 0.006 CYP3A5 0.52 <.001 0.66 0.003 CYR61 0.64 0.004 0.68 0.005 DDR2 0.57 0.002 0.73 0.004 DES 0.34 <.001 0.58 <.001 DLGAP1 0.54 <.001 0.62 <.001 DNM3 0.67 0.004 DPP4 0.41 <.001 0.53 <.001 DPT 0.28 <.001 0.48 <.001 DUSP1 0.59 <.001 0.63 <.001 EDNRA 0.64 0.004 0.74 0.008 EGF 0.71 0.012 EGR1 0.59 <.001 0.67 0.009 EGR3 0.72 0.026 0.71 0.025 EIF5 0.76 0.025 ELK4 0.58 0.001 0.70 0.008 ENPP2 0.66 0.002 0.70 0.005 EPHA3 0.65 0.006 EPHB2 0.60 <.001 0.78 0.023 EPHB4 0.75 0.046 0.73 0.006 ERBB3 0.76 0.040 0.75 0.013 ERBB4 0.74 0.023 ERCC1 0.63 <.001 0.77 0.016 FAAH 0.67 0.003 0.71 0.010 FAM107A 0.35 <.001 0.59 <.001 FAM13C 0.37 <.001 0.48 <.001 FAS 0.73 0.019 0.72 0.008 FGF10 0.53 <.001 0.58 <.001 FGF7 0.52 <.001 0.59 <.001 FGFR2 0.60 <.001 0.59 <.001 FKBP5 0.70 0.039 0.68 0.003 FLNA 0.39 <.001 0.56 <.001 FLNC 0.33 <.001 0.52 <.001 FOS 0.58 <.001 0.66 0.005 FOXO1 0.57 <.001 0.67 <.001 FOXQ1 0.74 0.023 GADD45B 0.62 0.002 0.71 0.010 GHR 0.62 0.002 0.72 0.009 GNRH1 0.74 0.049 0.75 0.026 GPM6B 0.48 <.001 0.68 <.001 GPS1 0.68 0.003 GSN 0.46 <.001 0.77 0.027 GSTM1 0.44 <.001 0.62 <.001 GSTM2 0.29 <.001 0.49 <.001 HGD 0.77 0.020 HIRIP3 0.75 0.034 HK1 0.48 <.001 0.66 0.001 HLF 0.42 <.001 0.55 <.001 HNF1B 0.67 0.006 0.74 0.010 HPS1 0.66 0.001 0.65 <.001 HSP90AB1 0.75 0.042 HSPA5 0.70 0.011 HSPB2 0.52 <.001 0.70 0.004 IGF1 0.35 <.001 0.59 <.001 IGF2 0.48 <.001 0.70 0.005 IGFBP2 0.61 <.001 0.77 0.044 IGFBP5 0.63 <.001 IGFBP6 0.45 <.001 0.64 <.001 IL6ST 0.55 0.004 0.63 <.001 ILK 0.40 <.001 0.57 <.001 ING5 0.56 <.001 0.78 0.033 ITGA1 0.56 0.004 0.61 <.001 ITGA3 0.78 0.035 ITGA5 0.71 0.019 0.75 0.017 ITGA7 0.37 <.001 0.52 <.001 ITGB3 0.63 0.003 0.70 0.005 ITPR1 0.46 <.001 0.64 <.001 ITPR3 0.70 0.013 ITSN1 0.62 0.001 JUN 0.48 <.001 0.60 <.001 JUNB 0.72 0.025 KIT 0.51 <.001 0.68 0.007 KLC1 0.58 <.001 KLK1 0.69 0.028 0.66 0.003 KLK2 0.60 <.001 KLK3 0.63 <.001 0.69 0.012 KRT15 0.56 <.001 0.60 <.001 KRT18 0.74 0.034 KRT5 0.64 <.001 0.62 <.001 LAMA4 0.47 <.001 0.73 0.010 LAMB3 0.73 0.018 0.69 0.003 LGALS3 0.59 0.003 0.54 <.001 LIG3 0.75 0.044 MAP3K7 0.66 0.003 0.79 0.031 MCM3 0.73 0.013 0.80 0.034 MGMT 0.61 0.001 0.71 0.007 MGST1 0.75 0.017 MLXIP 0.70 0.013 MMP2 0.57 <.001 0.72 0.010 MMP7 0.69 0.009 MPPED2 0.70 0.009 0.59 <.001 MSH6 0.78 0.046 MTA1 0.69 0.007 MTSS1 0.55 <.001 0.54 <.001 MYBPC1 0.45 <.001 0.45 <.001 NCAM1 0.51 <.001 0.65 <.001 NCAPD3 0.42 <.001 0.53 <.001 NCOR2 0.68 0.002 NDUFS5 0.66 0.001 0.70 0.013 NEXN 0.48 <.001 0.62 <.001 NFAT5 0.55 <.001 0.67 0.001 NFKBIA 0.79 0.048 NRG1 0.58 0.001 0.62 0.001 OLFML3 0.42 <.001 0.58 <.001 OMD 0.67 0.004 0.71 0.004 OR51E2 0.65 <.001 0.76 0.007 PAGE4 0.27 <.001 0.46 <.001 PCA3 0.68 0.004 PCDHGB7 0.70 0.025 0.65 <.001 PGF 0.62 0.001 PGR 0.63 0.028 PHTF2 0.69 0.033 PLP2 0.54 <.001 0.71 0.003 PPAP2B 0.41 <.001 0.54 <.001 PPP1R12A 0.48 <.001 0.60 <.001 PRIMA1 0.62 0.003 0.65 <.001 PRKAR1B 0.70 0.009 PRKAR2B 0.79 0.038 PRKCA 0.37 <.001 0.55 <.001 PRKCB 0.47 <.001 0.56 <.001 PTCH1 0.70 0.021 PTEN 0.66 0.010 0.64 <.001 PTGER3 0.76 0.015 PTGS2 0.70 0.013 0.68 0.005 PTH1R 0.48 <.001 PTK2B 0.67 0.014 0.69 0.002 PYCARD 0.72 0.023 RAB27A 0.76 0.017 RAGE 0.77 0.040 0.57 <.001 RARB 0.66 0.002 0.69 0.002 RECK 0.65 <.001 RHOA 0.73 0.043 RHOB 0.61 0.005 0.62 <.001 RND3 0.63 0.006 0.66 <.001 SDHC 0.69 0.002 SEC23A 0.61 <.001 0.74 0.010 SEMA3A 0.49 <.001 0.55 <.001 SERPINA3 0.70 0.034 0.75 0.020 SH3RF2 0.33 <.001 0.42 <.001 SLC22A3 0.23 <.001 0.37 <.001 SMAD4 0.33 <.001 0.39 <.001 SMARCC2 0.62 0.003 0.74 0.008 SMO 0.53 <.001 0.73 0.009 SORBS1 0.40 <.001 0.55 <.001 SPARCL1 0.42 <.001 0.63 <.001 SRD5A2 0.28 <.001 0.37 <.001 ST5 0.52 <.001 0.63 <.001 STAT5A 0.60 <.001 0.75 0.020 STAT5B 0.54 <.001 0.65 <.001 STS 0.78 0.035 SUMO1 0.75 0.017 0.71 0.002 SVIL 0.45 <.001 0.62 <.001 TARP 0.72 0.017 TGFB1I1 0.37 <.001 0.53 <.001 TGFB2 0.61 0.025 0.59 <.001 TGFB3 0.46 <.001 0.60 <.001 TIMP2 0.62 0.001 TIMP3 0.55 <.001 0.76 0.019 TMPRSS2 0.71 0.014 TNF 0.65 0.010 TNFRSF10A 0.71 0.014 0.74 0.010 TNFRSF10B 0.74 0.030 0.73 0.016 TNFSF10 0.69 0.004 TP53 0.73 0.011 TP63 0.62 <.001 0.68 0.003 TPM1 0.43 <.001 0.47 <.001 TPM2 0.30 <.001 0.47 <.001 TPP2 0.58 <.001 0.69 0.001 TRA2A 0.71 0.006 TRAF3IP2 0.50 <.001 0.63 <.001 TRO 0.40 <.001 0.59 <.001 TRPC6 0.73 0.030 TRPV6 0.80 0.047 VCL 0.44 <.001 0.55 <.001 VEGFB 0.73 0.029 VIM 0.72 0.013 VTI1B 0.78 0.046 WDR19 0.65 <.001 WFDC1 0.50 <.001 0.72 0.010 YY1 0.75 0.045 ZFHX3 0.52 <.001 0.54 <.001 ZFP36 0.65 0.004 0.69 0.012 ZNF827 0.59 <.001 0.69 0.004

To identify genes associated with recurrence (cRFI, bRFI) in the primary and the highest Gleason pattern, each of 727 genes were analyzed in univariate models using specimens A1 and B2 (see Table 2, above). Tables 4A and 4B provide genes that were associated, positively or negatively, with cRFI and/or bRFI in the primary and/or highest Gleason pattern. Increased expression of genes in Table 4A is negatively associated with good prognosis, while increased expression of genes in Table 4B is positively associated with good prognosis.

TABLE 4A Genes significantly (p < 0.05) associated with cRFI or bRFI in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) cRFI cRFI bRFI bRFI Table 4A Primary Highest Primary Highest Official Pattern Pattern Pattern Pattern Symbol HR p-value HR p-value HR p-value HR p-value AKR1C3 1.304 0.022 1.312 0.013 ANLN 1.379 0.002 1.579 <.001 1.465 <.001 1.623 <.001 AQP2 1.184 0.027 1.276 <.001 ASAP2 1.442 0.006 ASPN 2.272 <.001 2.106 <.001 1.861 <.001 1.895 <.001 ATP5E 1.414 0.013 1.538 <.001 BAG5 1.263 0.044 BAX 1.332 0.026 1.327 0.012 1.438 0.002 BGN 1.947 <.001 2.061 <.001 1.339 0.017 BIRC5 1.497 <.001 1.567 <.001 1.478 <.001 1.575 <.001 BMP6 1.705 <.001 2.016 <.001 1.418 0.004 1.541 <.001 BMPR1B 1.401 0.013 1.325 0.016 BRCA2 1.259 0.007 BUB1 1.411 <.001 1.435 <.001 1.352 <.001 1.242 0.002 CADPS 1.387 0.009 1.294 0.027 CCNB1 1.296 0.016 1.376 0.002 CCNE2 1.468 <.001 1.649 <.001 1.729 <.001 1.563 <.001 CD276 1.678 <.001 1.832 <.001 1.581 <.001 1.385 0.002 CDC20 1.547 <.001 1.671 <.001 1.446 <.001 1.540 <.001 CDC6 1.400 0.003 1.290 0.030 1.403 0.002 1.276 0.019 CDH7 1.403 0.003 1.413 0.002 CDKN2B 1.569 <.001 1.752 <.001 1.333 0.017 1.347 0.006 CDKN2C 1.612 <.001 1.780 <.001 1.323 0.005 1.335 0.004 CDKN3 1.384 <.001 1.255 0.024 1.285 0.003 1.216 0.028 CENPF 1.578 <.001 1.692 <.001 1.740 <.001 1.705 <.001 CKS2 1.390 0.007 1.418 0.005 1.291 0.018 CLTC 1.368 0.045 COL1A1 1.873 <.001 2.103 <.001 1.491 <.001 1.472 <.001 COL1A2 1.462 0.001 COL3A1 1.827 <.001 2.005 <.001 1.302 0.012 1.298 0.018 COL4A1 1.490 0.002 1.613 <.001 COL8A1 1.692 <.001 1.926 <.001 1.307 0.013 1.317 0.010 CRISP3 1.425 0.001 1.467 <.001 1.242 0.045 CTHRC1 1.505 0.002 2.025 <.001 1.425 0.003 1.369 0.005 CTNND2 1.412 0.003 CXCR4 1.312 0.023 1.355 0.008 DDIT4 1.543 <.001 1.763 <.001 DYNLL1 1.290 0.039 1.201 0.004 EIF3H 1.428 0.012 ENY2 1.361 0.014 1.392 0.008 1.371 0.001 EZH2 1.311 0.010 F2R 1.773 <.001 1.695 <.001 1.495 <.001 1.277 0.018 FADD 1.292 0.018 FAM171B 1.285 0.036 FAP 1.455 0.004 1.560 0.001 1.298 0.022 1.274 0.038 FASN 1.263 0.035 FCGR3A 1.654 <.001 1.253 0.033 1.350 0.007 FGF5 1.219 0.030 GNPTAB 1.388 0.007 1.503 0.003 1.355 0.005 1.434 0.002 GPR68 1.361 0.008 GREM1 1.470 0.003 1.716 <.001 1.421 0.003 1.316 0.017 HDAC1 1.290 0.025 HDAC9 1.395 0.012 HRAS 1.424 0.006 1.447 0.020 HSD17B4 1.342 0.019 1.282 0.026 1.569 <.001 1.390 0.002 HSPA8 1.290 0.034 IGFBP3 1.333 0.022 1.442 0.003 1.253 0.040 1.323 0.005 INHBA 2.368 <.001 2.765 <.001 1.466 0.002 1.671 <.001 JAG1 1.359 0.006 1.367 0.005 1.259 0.024 KCNN2 1.361 0.011 1.413 0.005 1.312 0.017 1.281 0.030 KHDRBS3 1.387 0.006 1.601 <.001 1.573 <.001 1.353 0.006 KIAA0196 1.249 0.037 KIF4A 1.212 0.016 1.149 0.040 1.278 0.003 KLK14 1.167 0.023 1.180 0.007 KPNA2 1.425 0.009 1.353 0.005 1.305 0.019 KRT75 1.164 0.028 LAMA3 1.327 0.011 LAMB1 1.347 0.019 LAMC1 1.555 0.001 1.310 0.030 1.349 0.014 LIMS1 1.275 0.022 LOX 1.358 0.003 1.410 <.001 LTBP2 1.396 0.009 1.656 <.001 1.278 0.022 LUM 1.315 0.021 MANF 1.660 <.001 1.323 0.011 MCM2 1.345 0.011 1.387 0.014 MCM6 1.307 0.023 1.352 0.008 1.244 0.039 MELK 1.293 0.014 1.401 <.001 1.501 <.001 1.256 0.012 MMP11 1.680 <.001 1.474 <.001 1.489 <.001 1.257 0.030 MRPL13 1.260 0.025 MSH2 1.295 0.027 MYBL2 1.664 <.001 1.670 <.001 1.399 <.001 1.431 <.001 MYO6 1.301 0.033 NETO2 1.412 0.004 1.302 0.027 1.298 0.009 NFKB1 1.236 0.050 NOX4 1.492 <.001 1.507 0.001 1.555 <.001 1.262 0.019 NPM1 1.287 0.036 NRIP3 1.219 0.031 1.218 0.018 NRP1 1.482 0.002 1.245 0.041 OLFML2B 1.362 0.015 OR51E1 1.531 <.001 1.488 0.003 PAK6 1.269 0.033 PATE1 1.308 <.001 1.332 <.001 1.164 0.044 PCNA 1.278 0.020 PEX10 1.436 0.005 1.393 0.009 PGD 1.298 0.048 1.579 <.001 PGK1 1.274 0.023 1.262 0.009 PLA2G7 1.315 0.011 1.346 0.005 PLAU 1.319 0.010 PLK1 1.309 0.021 1.563 <.001 1.410 0.002 1.372 0.003 PLOD2 1.284 0.019 1.272 0.014 1.332 0.005 POSTN 1.599 <.001 1.514 0.002 1.391 0.005 PPP3CA 1.402 0.007 1.316 0.018 PSMD13 1.278 0.040 1.297 0.033 1.279 0.017 1.373 0.004 PTK6 1.640 <.001 1.932 <.001 1.369 0.001 1.406 <.001 PTTG1 1.409 <.001 1.510 <.001 1.347 0.001 1.558 <.001 RAD21 1.315 0.035 1.402 0.004 1.589 <.001 1.439 <.001 RAF1 1.503 0.002 RALA 1.521 0.004 1.403 0.007 1.563 <.001 1.229 0.040 RALBP1 1.277 0.033 RGS7 1.154 0.015 1.266 0.010 RRM1 1.570 0.001 1.602 <.001 RRM2 1.368 <.001 1.289 0.004 1.396 <.001 1.230 0.015 SAT1 1.482 0.016 1.403 0.030 SDC1 1.340 0.018 1.396 0.018 SEC14L1 1.260 0.048 1.360 0.002 SESN3 1.485 <.001 1.631 <.001 1.232 0.047 1.292 0.014 SFRP4 1.800 <.001 1.814 <.001 1.496 <.001 1.289 0.027 SHMT2 1.807 <.001 1.658 <.001 1.673 <.001 1.548 <.001 SKIL 1.327 0.008 SLC25A21 1.398 0.001 1.285 0.018 SOX4 1.286 0.020 1.280 0.030 SPARC 1.539 <.001 1.842 <.001 1.269 0.026 SPP1 1.322 0.022 SQLE 1.359 0.020 1.270 0.036 STMN1 1.402 0.007 1.446 0.005 1.279 0.031 SULF1 1.587 <.001 TAF2 1.273 0.027 TFDP1 1.328 0.021 1.400 0.005 1.416 0.001 THBS2 1.812 <.001 1.960 <.001 1.320 0.012 1.256 0.038 THY1 1.362 0.020 1.662 <.001 TK1 1.251 0.011 1.377 <.001 1.401 <.001 TOP2A 1.670 <.001 1.920 <.001 1.869 <.001 1.927 <.001 TPD52 1.324 0.011 1.366 0.002 1.351 0.005 TPX2 1.884 <.001 2.154 <.001 1.874 <.001 1.794 <.001 UAP1 1.244 0.044 UBE2C 1.403 <.001 1.541 <.001 1.306 0.002 1.323 <.001 UBE2T 1.667 <.001 1.282 0.023 1.502 <.001 1.298 0.005 UGT2B15 1.295 0.001 1.275 0.002 UGT2B17 1.294 0.025 UHRF1 1.454 <.001 1.531 <.001 1.257 0.029 VCPIP1 1.390 0.009 1.414 0.004 1.294 0.021 1.283 0.021 WNT5A 1.274 0.038 1.298 0.020 XIAP 1.464 0.006 ZMYND8 1.277 0.048 ZWINT 1.259 0.047

TABLE 4B Genes significantly (p < 0.05) associated with cRFI or bRFI in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) cRFI cRFI bRFI bRFI Table 4B Primary Highest Primary Highest Official Pattern Pattern Pattern Pattern Symbol HR p-value HR p-value HR p-value HR p-value AAMP 0.564 <.001 0.571 <.001 0.764 0.037 0.786 0.034 ABCA5 0.755 <.001 0.695 <.001 0.800 0.006 ABCB1 0.777 0.026 ABCG2 0.788 0.033 0.784 0.040 0.803 0.018 0.750 0.004 ABHD2 0.734 0.011 ACE 0.782 0.048 ACOX2 0.639 <.001 0.631 <.001 0.713 <.001 0.716 0.002 ADH5 0.625 <.001 0.637 <.001 0.753 0.026 AKAP1 0.764 0.006 0.800 0.005 0.837 0.046 AKR1C1 0.773 0.033 0.802 0.032 AKT1 0.714 0.005 AKT3 0.811 0.015 0.809 0.021 ALDH1A2 0.606 <.001 0.498 <.001 0.613 <.001 0.624 <.001 AMPD3 0.793 0.024 ANPEP 0.584 <.001 0.493 <.001 ANXA2 0.753 0.013 0.781 0.036 0.762 0.008 0.795 0.032 APRT 0.758 0.026 0.780 0.044 0.746 0.008 ATXN1 0.673 0.001 0.776 0.029 0.809 0.031 0.812 0.043 AXIN2 0.674 <.001 0.571 <.001 0.776 0.005 0.757 0.005 AZGP1 0.585 <.001 0.652 <.001 0.664 <.001 0.746 <.001 BAD 0.765 0.023 BCL2 0.788 0.033 0.778 0.036 BDKRB1 0.728 0.039 BIK 0.712 0.005 BIN1 0.607 <.001 0.724 0.002 0.726 <.001 0.834 0.034 BTG3 0.847 0.034 BTRC 0.688 0.001 0.713 0.003 C7 0.589 <.001 0.639 <.001 0.629 <.001 0.691 <.001 CADM1 0.546 <.001 0.529 <.001 0.743 0.008 0.769 0.015 CASP1 0.769 0.014 0.799 0.028 0.799 0.010 0.815 0.018 CAV1 0.736 0.011 0.711 0.005 0.675 <.001 0.743 0.006 CAV2 0.636 0.010 0.648 0.012 0.685 0.012 CCL2 0.759 0.029 0.764 0.024 CCNH 0.689 <.001 0.700 <.001 CD164 0.664 <.001 0.651 <.001 CD1A 0.687 0.004 CD44 0.545 <.001 0.600 <.001 0.788 0.018 0.799 0.023 CD82 0.771 0.009 0.748 0.004 CDC25B 0.755 0.006 0.817 0.025 CDK14 0.845 0.043 CDK2 0.819 0.032 CDK3 0.733 0.005 0.772 0.006 0.838 0.017 CDKN1A 0.766 0.041 CDKN1C 0.662 <.001 0.712 0.002 0.693 <.001 0.761 0.009 CHN1 0.788 0.036 COL6A1 0.608 <.001 0.767 0.013 0.706 <.001 0.775 0.007 CSF1 0.626 <.001 0.709 0.003 CSK 0.837 0.029 CSRP1 0.793 0.024 0.782 0.019 CTNNB1 0.898 0.042 0.885 <.001 CTSB 0.701 0.004 0.713 0.007 0.715 0.002 0.803 0.038 CTSK 0.815 0.042 CXCL12 0.652 <.001 0.802 0.044 0.711 0.001 CYP3A5 0.463 <.001 0.436 <.001 0.727 0.003 CYR61 0.652 0.002 0.676 0.002 DAP 0.761 0.026 0.775 0.025 0.802 0.048 DARC 0.725 0.005 0.792 0.032 DDR2 0.719 0.001 0.763 0.008 DES 0.619 <.001 0.737 0.005 0.638 <.001 0.793 0.017 DHRS9 0.642 0.003 DHX9 0.888 <.001 DLC1 0.710 0.007 0.715 0.009 DLGAP1 0.613 <.001 0.551 <.001 0.779 0.049 DNM3 0.679 <.001 0.812 0.037 DPP4 0.591 <.001 0.613 <.001 0.761 0.003 DPT 0.613 <.001 0.576 <.001 0.647 <.001 0.677 <.001 DUSP1 0.662 0.001 0.665 0.001 0.785 0.024 DUSP6 0.713 0.005 0.668 0.002 EDNRA 0.702 0.002 0.779 0.036 EGF 0.738 0.028 EGR1 0.569 <.001 0.577 <.001 0.782 0.022 EGR3 0.601 <.001 0.619 <.001 0.800 0.038 EIF2S3 0.756 0.015 EIF5 0.776 0.023 0.787 0.028 ELK4 0.628 <.001 0.658 <.001 EPHA2 0.720 0.011 0.663 0.004 EPHA3 0.727 0.003 0.772 0.005 ERBB2 0.786 0.019 0.738 0.003 0.815 0.041 ERBB3 0.728 0.002 0.711 0.002 0.828 0.043 0.813 0.023 ERCC1 0.771 0.023 0.725 0.007 0.806 0.049 0.704 0.002 EREG 0.754 0.016 0.777 0.034 ESR2 0.731 0.026 FAAH 0.708 0.004 0.758 0.012 0.784 0.031 0.774 0.007 FAM107A 0.517 <.001 0.576 <.001 0.642 <.001 0.656 <.001 FAM13C 0.568 <.001 0.526 <.001 0.739 0.002 0.639 <.001 FAS 0.755 0.014 FASLG 0.706 0.021 FGF10 0.653 <.001 0.685 <.001 0.766 0.022 FGF17 0.746 0.023 0.781 0.015 0.805 0.028 FGF7 0.794 0.030 0.820 0.037 0.811 0.040 FGFR2 0.683 <.001 0.686 <.001 0.674 <.001 0.703 <.001 FKBP5 0.676 0.001 FLNA 0.653 <.001 0.741 0.010 0.682 <.001 0.771 0.016 FLNC 0.751 0.029 0.779 0.047 0.663 <.001 0.725 <.001 FLT1 0.799 0.044 FOS 0.566 <.001 0.543 <.001 0.757 0.006 FOXO1 0.816 0.039 0.798 0.023 FOXQ1 0.753 0.017 0.757 0.024 0.804 0.018 FYN 0.779 0.031 GADD45B 0.590 <.001 0.619 <.001 GDF15 0.759 0.019 0.794 0.048 GHR 0.702 0.005 0.630 <.001 0.673 <.001 0.590 <.001 GNRH1 0.742 0.014 GPM6B 0.653 <.001 0.633 <.001 0.696 <.001 0.768 0.007 GSN 0.570 <.001 0.697 0.001 0.697 <.001 0.758 0.005 GSTM1 0.612 <.001 0.588 <.001 0.718 <.001 0.801 0.020 GSTM2 0.540 <.001 0.630 <.001 0.602 <.001 0.706 <.001 HGD 0.796 0.020 0.736 0.002 HIRIP3 0.753 0.011 0.824 0.050 HK1 0.684 <.001 0.683 <.001 0.799 0.011 0.804 0.014 HLA-G 0.726 0.022 HLF 0.555 <.001 0.582 <.001 0.703 <.001 0.702 <.001 HNF1B 0.690 <.001 0.585 <.001 HPS1 0.744 0.003 0.784 0.020 0.836 0.047 HSD3B2 0.733 0.016 HSP90AB1 0.801 0.036 HSPA5 0.776 0.034 HSPB1 0.813 0.020 HSPB2 0.762 0.037 0.699 0.002 0.783 0.034 HSPG2 0.794 0.044 ICAM1 0.743 0.024 0.768 0.040 IER3 0.686 0.002 0.663 <.001 IFIT1 0.649 <.001 0.761 0.026 IGF1 0.634 <.001 0.537 <.001 0.696 <.001 0.688 <.001 IGF2 0.732 0.004 IGFBP2 0.548 <.001 0.620 <.001 IGFBP5 0.681 <.001 IGFBP6 0.577 <.001 0.675 <.001 IL1B 0.712 0.005 0.742 0.009 IL6 0.763 0.028 IL6R 0.791 0.039 IL6ST 0.585 <.001 0.639 <.001 0.730 0.002 0.768 0.006 IL8 0.624 <.001 0.662 0.001 ILK 0.712 0.009 0.728 0.012 0.790 0.047 0.790 0.042 ING5 0.625 <.001 0.658 <.001 0.728 0.002 ITGA5 0.728 0.006 0.803 0.039 ITGA6 0.779 0.007 0.775 0.006 ITGA7 0.584 <.001 0.700 0.001 0.656 <.001 0.786 0.014 ITGAD 0.657 0.020 ITGB4 0.718 0.007 0.689 <.001 0.818 0.041 ITGB5 0.801 0.050 ITPR1 0.707 0.001 JUN 0.556 <.001 0.574 <.001 0.754 0.008 JUNB 0.730 0.017 0.715 0.010 KIT 0.644 0.004 0.705 0.019 0.605 <.001 0.659 0.001 KLC1 0.692 0.003 0.774 0.024 0.747 0.008 KLF6 0.770 0.032 0.776 0.039 KLK1 0.646 <.001 0.652 0.001 0.784 0.037 KLK10 0.716 0.006 KLK2 0.647 <.001 0.628 <.001 0.786 0.009 KLK3 0.706 <.001 0.748 <.001 0.845 0.018 KRT1 0.734 0.024 KRT15 0.627 <.001 0.526 <.001 0.704 <.001 0.782 0.029 KRT18 0.624 <.001 0.617 <.001 0.738 0.005 0.760 0.005 KRT5 0.640 <.001 0.550 <.001 0.740 <.001 0.798 0.023 KRT8 0.716 0.006 0.744 0.008 L1CAM 0.738 0.021 0.692 0.009 0.761 0.036 LAG3 0.741 0.013 0.729 0.011 LAMA4 0.686 0.011 0.592 0.003 LAMA5 0.786 0.025 LAMB3 0.661 <.001 0.617 <.001 0.734 <.001 LGALS3 0.618 <.001 0.702 0.001 0.734 0.001 0.793 0.012 LIG3 0.705 0.008 0.615 <.001 LRP1 0.786 0.050 0.795 0.023 0.770 0.009 MAP3K7 0.789 0.003 MGMT 0.632 <.001 0.693 <.001 MICA 0.781 0.014 0.653 <.001 0.833 0.043 MPPED2 0.655 <.001 0.597 <.001 0.719 <.001 0.759 0.006 MSH6 0.793 0.015 MTSS1 0.613 <.001 0.746 0.008 MVP 0.792 0.028 0.795 0.045 0.819 0.023 MYBPC1 0.648 <.001 0.496 <.001 0.701 <.001 0.629 <.001 NCAM1 0.773 0.015 NCAPD3 0.574 <.001 0.463 <.001 0.679 <.001 0.640 <.001 NEXN 0.701 0.002 0.791 0.035 0.725 0.002 0.781 0.016 NFAT5 0.515 <.001 0.586 <.001 0.785 0.017 NFATC2 0.753 0.023 NFKBIA 0.778 0.037 NRG1 0.644 0.004 0.696 0.017 0.698 0.012 OAZ1 0.777 0.034 0.775 0.022 OLFML3 0.621 <.001 0.720 0.001 0.600 <.001 0.626 <.001 OMD 0.706 0.003 OR51E2 0.820 0.037 0.798 0.027 PAGE4 0.549 <.001 0.613 <.001 0.542 <.001 0.628 <.001 PCA3 0.684 <.001 0.635 <.001 PCDHGB7 0.790 0.045 0.725 0.002 0.664 <.001 PGF 0.753 0.017 PGR 0.740 0.021 0.728 0.018 PIK3CG 0.803 0.024 PLAUR 0.778 0.035 PLG 0.728 0.028 PPAP2B 0.575 <.001 0.629 <.001 0.643 <.001 0.699 <.001 PPP1R12A 0.647 <.001 0.683 0.002 0.782 0.023 0.784 0.030 PRIMA1 0.626 <.001 0.658 <.001 0.703 0.002 0.724 0.003 PRKCA 0.642 <.001 0.799 0.029 0.677 0.001 0.776 0.006 PRKCB 0.675 0.001 0.648 <.001 0.747 0.006 PROM1 0.603 0.018 0.659 0.014 0.493 0.008 PTCH1 0.680 0.001 0.753 0.010 0.789 0.018 PTEN 0.732 0.002 0.747 0.005 0.744 <.001 0.765 0.002 PTGS2 0.596 <.001 0.610 <.001 PTH1R 0.767 0.042 0.775 0.028 0.788 0.047 PTHLH 0.617 0.002 0.726 0.025 0.668 0.002 0.718 0.007 PTK2B 0.744 0.003 0.679 <.001 0.766 0.002 0.726 <.001 PTPN1 0.760 0.020 0.780 0.042 PYCARD 0.748 0.012 RAB27A 0.708 0.004 RAB30 0.755 0.008 RAGE 0.817 0.048 RAP1B 0.818 0.050 RARB 0.757 0.007 0.677 <.001 0.789 0.007 0.746 0.003 RASSF1 0.816 0.035 RHOB 0.725 0.009 0.676 0.001 0.793 0.039 RLN1 0.742 0.033 0.762 0.040 RND3 0.636 <.001 0.647 <.001 RNF114 0.749 0.011 SDC2 0.721 0.004 SDHC 0.725 0.003 0.727 0.006 SEMA3A 0.757 0.024 0.721 0.010 SERPINA3 0.716 0.008 0.660 0.001 SERPINB5 0.747 0.031 0.616 0.002 SH3RF2 0.577 <.001 0.458 <.001 0.702 <.001 0.640 <.001 SLC22A3 0.565 <.001 0.540 <.001 0.747 0.004 0.756 0.007 SMAD4 0.546 <.001 0.573 <.001 0.636 <.001 0.627 <.001 SMARCD1 0.718 <.001 0.775 0.017 SMO 0.793 0.029 0.754 0.021 0.718 0.003 SOD1 0.757 0.049 0.707 0.006 SORBS1 0.645 <.001 0.716 0.003 0.693 <.001 0.784 0.025 SPARCL1 0.821 0.028 0.829 0.014 0.781 0.030 SPDEF 0.778 <.001 SPINT1 0.732 0.009 0.842 0.026 SRC 0.647 <.001 0.632 <.001 SRD5A1 0.813 0.040 SRD5A2 0.489 <.001 0.533 <.001 0.544 <.001 0.611 <.001 ST5 0.713 0.002 0.783 0.011 0.725 <.001 0.827 0.025 STAT3 0.773 0.037 0.759 0.035 STAT5A 0.695 <.001 0.719 0.002 0.806 0.020 0.783 0.008 STAT5B 0.633 <.001 0.655 <.001 0.814 0.028 SUMO1 0.790 0.015 SVIL 0.659 <.001 0.713 0.002 0.711 0.002 0.779 0.010 TARP 0.800 0.040 TBP 0.761 0.010 TFF3 0.734 0.010 0.659 <.001 TGFB1I1 0.618 <.001 0.693 0.002 0.637 <.001 0.719 0.004 TGFB2 0.679 <.001 0.747 0.005 0.805 0.030 TGFB3 0.791 0.037 TGFBR2 0.778 0.035 TIMP3 0.751 0.011 TMPRSS2 0.745 0.003 0.708 <.001 TNF 0.670 0.013 0.697 0.015 TNFRSF10A 0.780 0.018 0.752 0.006 0.817 0.032 TNFRSF10B 0.576 <.001 0.655 <.001 0.766 0.004 0.778 0.002 TNFRSF18 0.648 0.016 0.759 0.034 TNFSF10 0.653 <.001 0.667 0.004 TP53 0.729 0.003 TP63 0.759 0.016 0.636 <.001 0.698 <.001 0.712 0.001 TPM1 0.778 0.048 0.743 0.012 0.783 0.032 0.811 0.046 TPM2 0.578 <.001 0.634 <.001 0.611 <.001 0.710 0.001 TPP2 0.775 0.037 TRAF3IP2 0.722 0.002 0.690 <.001 0.792 0.021 0.823 0.049 TRO 0.744 0.003 0.725 0.003 0.765 0.002 0.821 0.041 TUBB2A 0.639 <.001 0.625 <.001 TYMP 0.786 0.039 VCL 0.594 <.001 0.657 0.001 0.682 <.001 VEGFA 0.762 0.024 VEGFB 0.795 0.037 VIM 0.739 0.009 0.791 0.021 WDR19 0.776 0.015 WFDC1 0.746 <.001 YY1 0.683 0.001 0.728 0.002 ZFHX3 0.684 <.001 0.661 <.001 0.801 0.010 0.762 0.001 ZFP36 0.605 <.001 0.579 <.001 0.815 0.043 ZNF827 0.624 <.001 0.730 0.007 0.738 0.004

Tables 5A and 5B provide genes that were significantly associated (p<0.05), positively or negatively, with recurrence (cRFI, bRFI) after adjusting for AUA risk group in the primary and/or highest Gleason pattern. Increased expression of genes in Table 5A is negatively associated with good prognosis, while increased expression of genes in Table 5B is positively associated with good prognosis.

TABLE 5A Gene significantly (p < 0.05) associated with cRFI or bRFI after adjustment for AUA risk group in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) > 1.0 (increased expression negatively associated with good prognosis) cRFI cRFI bRFI bRFI Table 5A Primary Highest Primary Highest Official Pattern Pattern Pattern Pattern Symbol HR p-value HR p-value HR p-value HR p-value AKR1C3 1.315 0.018 1.283 0.024 ALOX12 1.198 0.024 ANLN 1.406 <.001 1.519 <.001 1.485 <.001 1.632 <.001 AQP2 1.209 <.001 1.302 <.001 ASAP2 1.582 <.001 1.333 0.011 1.307 0.019 ASPN 1.872 <.001 1.741 <.001 1.638 <.001 1.691 <.001 ATP5E 1.309 0.042 1.369 0.012 BAG5 1.291 0.044 BAX 1.298 0.025 1.420 0.004 BGN 1.746 <.001 1.755 <.001 BIRC5 1.480 <.001 1.470 <.001 1.419 <.001 1.503 <.001 BMP6 1.536 <.001 1.815 <.001 1.294 0.033 1.429 0.001 BRCA2 1.184 0.037 BUB1 1.288 0.001 1.391 <.001 1.254 <.001 1.189 0.018 CACNA1D 1.313 0.029 CADPS 1.358 0.007 1.267 0.022 CASP3 1.251 0.037 CCNB1 1.261 0.033 1.318 0.005 CCNE2 1.345 0.005 1.438 <.001 1.606 <.001 1.426 <.001 CD276 1.482 0.002 1.668 <.001 1.451 <.001 1.302 0.011 CDC20 1.417 <.001 1.547 <.001 1.355 <.001 1.446 <.001 CDC6 1.340 0.011 1.265 0.046 1.367 0.002 1.272 0.025 CDH7 1.402 0.003 1.409 0.002 CDKN2B 1.553 <.001 1.746 <.001 1.340 0.014 1.369 0.006 CDKN2C 1.411 <.001 1.604 <.001 1.220 0.033 CDKN3 1.296 0.004 1.226 0.015 CENPF 1.434 0.002 1.570 <.001 1.633 <.001 1.610 <.001 CKS2 1.419 0.008 1.374 0.022 1.380 0.004 COL1A1 1.677 <.001 1.809 <.001 1.401 <.001 1.352 0.003 COL1A2 1.373 0.010 COL3A1 1.669 <.001 1.781 <.001 1.249 0.024 1.234 0.047 COL4A1 1.475 0.002 1.513 0.002 COL8A1 1.506 0.001 1.691 <.001 CRISP3 1.406 0.004 1.471 <.001 CTHRC1 1.426 0.009 1.793 <.001 1.311 0.019 CTNND2 1.462 <.001 DDIT4 1.478 0.003 1.783 <.001 1.236 0.039 DYNLL1 1.431 0.002 1.193 0.004 EIF3H 1.372 0.027 ENY2 1.325 0.023 1.270 0.017 ERG 1.303 0.041 EZH2 1.254 0.049 F2R 1.540 0.002 1.448 0.006 1.286 0.023 FADD 1.235 0.041 1.404 <.001 FAP 1.386 0.015 1.440 0.008 1.253 0.048 FASN 1.303 0.028 FCGR3A 1.439 0.011 1.262 0.045 FGF5 1.289 0.006 GNPTAB 1.290 0.033 1.369 0.022 1.285 0.018 1.355 0.008 GPR68 1.396 0.005 GREM1 1.341 0.022 1.502 0.003 1.366 0.006 HDAC1 1.329 0.016 HDAC9 1.378 0.012 HRAS 1.465 0.006 HSD17B4 1.442 <.001 1.245 0.028 IGFBP3 1.366 0.019 1.302 0.011 INHBA 2.000 <.001 2.336 <.001 1.486 0.002 JAG1 1.251 0.039 KCNN2 1.347 0.020 1.524 <.001 1.312 0.023 1.346 0.011 KHDRBS3 1.500 0.001 1.426 0.001 1.267 0.032 KIAA0196 1.272 0.028 KIF4A 1.199 0.022 1.262 0.004 KPNA2 1.252 0.016 LAMA3 1.332 0.004 1.356 0.010 LAMB1 1.317 0.028 LAMC1 1.516 0.003 1.302 0.040 1.397 0.007 LIMS1 1.261 0.027 LOX 1.265 0.016 1.372 0.001 LTBP2 1.477 0.002 LUM 1.321 0.020 MANF 1.647 <.001 1.284 0.027 MCM2 1.372 0.003 1.302 0.032 MCM3 1.269 0.047 MCM6 1.276 0.033 1.245 0.037 MELK 1.294 0.005 1.394 <.001 MKI67 1.253 0.028 1.246 0.029 MMP11 1.557 <.001 1.290 0.035 1.357 0.005 MRPL13 1.275 0.003 MSH2 1.355 0.009 MYBL2 1.497 <.001 1.509 <.001 1.304 0.003 1.292 0.007 MYO6 1.367 0.010 NDRG1 1.270 0.042 1.314 0.025 NEK2 1.338 0.020 1.269 0.026 NETO2 1.434 0.004 1.303 0.033 1.283 0.012 NOX4 1.413 0.006 1.308 0.037 1.444 <.001 NRIP3 1.171 0.026 NRP1 1.372 0.020 ODC1 1.450 <.001 OR51E1 1.559 <.001 1.413 0.008 PAK6 1.233 0.047 PATE1 1.262 <.001 1.375 <.001 1.143 0.034 1.191 0.036 PCNA 1.227 0.033 1.318 0.003 PEX10 1.517 <.001 1.500 0.001 PGD 1.363 0.028 1.316 0.039 1.652 <.001 PGK1 1.224 0.034 1.206 0.024 PIM1 1.205 0.042 PLA2G7 1.298 0.018 1.358 0.005 PLAU 1.242 0.032 PLK1 1.464 0.001 1.299 0.018 1.275 0.031 PLOD2 1.206 0.039 1.261 0.025 POSTN 1.558 0.001 1.356 0.022 1.363 0.009 PPP3CA 1.445 0.002 PSMD13 1.301 0.017 1.411 0.003 PTK2 1.318 0.031 PTK6 1.582 <.001 1.894 <.001 1.290 0.011 1.354 0.003 PTTG1 1.319 0.004 1.430 <.001 1.271 0.006 1.492 <.001 RAD21 1.278 0.028 1.435 0.004 1.326 0.008 RAF1 1.504 <.001 RALA 1.374 0.028 1.459 0.001 RGS7 1.203 0.031 RRM1 1.535 0.001 1.525 <.001 RRM2 1.302 0.003 1.197 0.047 1.342 <.001 SAT1 1.374 0.043 SDC1 1.344 0.011 1.473 0.008 SEC14L1 1.297 0.006 SESN3 1.337 0.002 1.495 <.001 1.223 0.038 SFRP4 1.610 <.001 1.542 0.002 1.370 0.009 SHMT2 1.567 0.001 1.522 <.001 1.485 0.001 1.370 <.001 SKIL 1.303 0.008 SLC25A21 1.287 0.020 1.306 0.017 SLC44A1 1.308 0.045 SNRPB2 1.304 0.018 SOX4 1.252 0.031 SPARC 1.445 0.004 1.706 <.001 1.269 0.026 SPP1 1.376 0.016 SQLE 1.417 0.007 1.262 0.035 STAT1 1.209 0.029 STMN1 1.315 0.029 SULF1 1.504 0.001 TAF2 1.252 0.048 1.301 0.019 TFDP1 1.395 0.010 1.424 0.002 THBS2 1.716 <.001 1.719 <.001 THY1 1.343 0.035 1.575 0.001 TK1 1.320 <.001 1.304 <.001 TOP2A 1.464 0.001 1.688 <.001 1.715 <.001 1.761 <.001 TPD52 1.286 0.006 1.258 0.023 TPX2 1.644 <.001 1.964 <.001 1.699 <.001 1.754 <.001 TYMS 1.315 0.014 UBE2C 1.270 0.019 1.558 <.001 1.205 0.027 1.333 <.001 UBE2G1 1.302 0.041 UBE2T 1.451 <.001 1.309 0.003 UGT2B15 1.222 0.025 UHRF1 1.370 0.003 1.520 <.001 1.247 0.020 VCPIP1 1.332 0.015 VTI1B 1.237 0.036 XIAP 1.486 0.008 ZMYND8 1.408 0.007 ZNF3 1.284 0.018 ZWINT 1.289 0.028

TABLE 5B Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for AUA risk group in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) < 1.0 (increased expression is positively associated with good prognosis) cRFI cRFI bRFI Primary Highest Primary bRFI Table 5B Pattern Pattern Pattern Highest Official p- p- p- Pattern Symbol HR value HR value HR value HR p-value AAMP 0.535 <.001 0.581 <.001 0.700 0.002 0.759 0.006 ABCA5 0.798 0.007 0.745 0.002 0.841 0.037 ABCC1 0.800 0.044 ABCC4 0.787 0.022 ABHD2 0.768 0.023 ACOX2 0.678 0.002 0.749 0.027 0.759 0.004 ADH5 0.645 <.001 0.672 0.001 AGTR1 0.780 0.030 AKAP1 0.815 0.045 0.758 <.001 AKT1 0.732 0.010 ALDH1A2 0.646 <.001 0.548 <.001 0.671 <.001 0.713 0.001 ANPEP 0.641 <.001 0.535 <.001 ANXA2 0.772 0.035 0.804 0.046 ATXN1 0.654 <.001 0.754 0.020 0.797 0.017 AURKA 0.788 0.030 AXIN2 0.744 0.005 0.655 <.001 AZGP1 0.656 <.001 0.676 <.001 0.754 0.001 0.791 0.004 BAD 0.700 0.004 BIN1 0.650 <.001 0.764 0.013 0.803 0.015 BTG3 0.836 0.025 BTRC 0.730 0.005 C7 0.617 <.001 0.680 <.001 0.667 <.001 0.755 0.005 CADM1 0.559 <.001 0.566 <.001 0.772 0.020 0.802 0.046 CASP1 0.781 0.030 0.779 0.021 0.818 0.027 0.828 0.036 CAV1 0.775 0.034 CAV2 0.677 0.019 CCL2 0.752 0.023 CCNH 0.679 <.001 0.682 <.001 CD164 0.721 0.002 0.724 0.005 CD1A 0.710 0.014 CD44 0.591 <.001 0.642 <.001 CD82 0.779 0.021 0.771 0.024 CDC25B 0.778 0.035 0.818 0.023 CDK14 0.788 0.011 CDK3 0.752 0.012 0.779 0.005 0.841 0.020 CDKN1A 0.770 0.049 0.712 0.014 CDKN1C 0.684 <.001 0.697 <.001 CHN1 0.772 0.031 COL6A1 0.648 <.001 0.807 0.046 0.768 0.004 CSF1 0.621 <.001 0.671 0.001 CTNNB1 0.905 0.008 CTSB 0.754 0.030 0.716 0.011 0.756 0.014 CXCL12 0.641 <.001 0.796 0.038 0.708 <.001 CYP3A5 0.503 <.001 0.528 <.001 0.791 0.028 CYR61 0.639 0.001 0.659 0.001 0.797 0.048 DARC 0.707 0.004 DDR2 0.750 0.011 DES 0.657 <.001 0.758 0.022 0.699 <.001 DHRS9 0.625 0.002 DHX9 0.846 <.001 DIAPH1 0.682 0.007 0.723 0.008 0.780 0.026 DLC1 0.703 0.005 0.702 0.008 DLGAP1 0.703 0.008 0.636 <.001 DNM3 0.701 0.001 0.817 0.042 DPP4 0.686 <.001 0.716 0.001 DPT 0.636 <.001 0.633 <.001 0.709 0.006 0.773 0.024 DUSP1 0.683 0.006 0.679 0.003 DUSP6 0.694 0.003 0.605 <.001 EDN1 0.773 0.031 EDNRA 0.716 0.007 EGR1 0.575 <.001 0.575 <.001 0.771 0.014 EGR3 0.633 0.002 0.643 <.001 0.792 0.025 EIF4E 0.722 0.002 ELK4 0.710 0.009 0.759 0.027 ENPP2 0.786 0.039 EPHA2 0.593 0.001 EPHA3 0.739 0.006 0.802 0.020 ERBB2 0.753 0.007 ERBB3 0.753 0.009 0.753 0.015 ERCC1 0.727 0.001 EREG 0.722 0.012 0.769 0.040 ESR1 0.742 0.015 FABP5 0.756 0.032 FAM107A 0.524 <.001 0.579 <.001 0.688 <.001 0.699 0.001 FAM13C 0.639 <.001 0.601 <.001 0.810 0.019 0.709 <.001 FAS 0.770 0.033 FASLG 0.716 0.028 0.683 0.017 FGF10 0.798 0.045 FGF17 0.718 0.018 0.793 0.024 0.790 0.024 FGFR2 0.739 0.007 0.783 0.038 0.740 0.004 FGFR4 0.746 0.050 FKBP5 0.689 0.003 FLNA 0.701 0.006 0.766 0.029 0.768 0.037 FLNC 0.755 <.001 0.820 0.022 FLT1 0.729 0.008 FOS 0.572 <.001 0.536 <.001 0.750 0.005 FOXQ1 0.778 0.033 0.820 0.018 FYN 0.708 0.006 GADD45B 0.577 <.001 0.589 <.001 GDF15 0.757 0.013 0.743 0.006 GHR 0.712 0.004 0.679 0.001 GNRH1 0.791 0.048 GPM6B 0.675 <.001 0.660 <.001 0.735 <.001 0.823 0.049 GSK3B 0.783 0.042 GSN 0.587 <.001 0.705 0.002 0.745 0.004 0.796 0.021 GSTM1 0.686 0.001 0.631 <.001 0.807 0.018 GSTM2 0.607 <.001 0.683 <.001 0.679 <.001 0.800 0.027 HIRIP3 0.692 <.001 0.782 0.007 HK1 0.724 0.002 0.718 0.002 HLF 0.580 <.001 0.571 <.001 0.759 0.008 0.750 0.004 HNF1B 0.669 <.001 HPS1 0.764 0.008 HSD17B10 0.802 0.045 HSD17B2 0.723 0.048 HSD3B2 0.709 0.010 HSP90AB1 0.780 0.034 0.809 0.041 HSPA5 0.738 0.017 HSPB1 0.770 0.006 0.801 0.032 HSPB2 0.788 0.035 ICAM1 0.728 0.015 0.716 0.010 IER3 0.735 0.016 0.637 <.001 0.802 0.035 IFIT1 0.647 <.001 0.755 0.029 IGF1 0.675 <.001 0.603 <.001 0.762 0.006 0.770 0.030 IGF2 0.761 0.011 IGFBP2 0.601 <.001 0.605 <.001 IGFBP5 0.702 <.001 IGFBP6 0.628 <.001 0.726 0.003 IL1B 0.676 0.002 0.716 0.004 IL6 0.688 0.005 0.766 0.044 IL6R 0.786 0.036 IL6ST 0.618 <.001 0.639 <.001 0.785 0.027 0.813 0.042 IL8 0.635 <.001 0.628 <.001 ILK 0.734 0.018 0.753 0.026 ING5 0.684 <.001 0.681 <.001 0.756 0.006 ITGA4 0.778 0.040 ITGA5 0.762 0.026 ITGA6 0.811 0.038 ITGA7 0.592 <.001 0.715 0.006 0.710 0.002 ITGAD 0.576 0.006 ITGB4 0.693 0.003 ITPR1 0.789 0.029 JUN 0.572 <.001 0.581 <.001 0.777 0.019 JUNB 0.732 0.030 0.707 0.016 KCTD12 0.758 0.036 KIT 0.691 0.009 0.738 0.028 KLC1 0.741 0.024 0.781 0.024 KLF6 0.733 0.018 0.727 0.014 KLK1 0.744 0.028 KLK2 0.697 0.002 0.679 <.001 KLK3 0.725 <.001 0.715 <.001 0.841 0.023 KRT15 0.660 <.001 0.577 <.001 0.750 0.002 KRT18 0.623 <.001 0.642 <.001 0.702 <.001 0.760 0.006 KRT2 0.740 0.044 KRT5 0.674 <.001 0.588 <.001 0.769 0.005 KRT8 0.768 0.034 L1CAM 0.737 0.036 LAG3 0.711 0.013 0.748 0.029 LAMA4 0.649 0.009 LAMB3 0.709 0.002 0.684 0.006 0.768 0.006 LGALS3 0.652 <.001 0.752 0.015 0.805 0.028 LIG3 0.728 0.016 0.667 <.001 LRP1 0.811 0.043 MDM2 0.788 0.033 MGMT 0.645 <.001 0.766 0.015 MICA 0.796 0.043 0.676 <.001 MPPED2 0.675 <.001 0.616 <.001 0.750 0.006 MRC1 0.788 0.028 MTSS1 0.654 <.001 0.793 0.036 MYBPC1 0.706 <.001 0.534 <.001 0.773 0.004 0.692 <.001 NCAPD3 0.658 <.001 0.566 <.001 0.753 0.011 0.733 0.009 NCOR1 0.838 0.045 NEXN 0.748 0.025 0.785 0.020 NFAT5 0.531 <.001 0.626 <.001 NFATC2 0.759 0.024 OAZ1 0.766 0.024 OLFML3 0.648 <.001 0.748 0.005 0.639 <.001 0.675 <.001 OR51E2 0.823 0.034 PAGE4 0.599 <.001 0.698 0.002 0.606 <.001 0.726 <.001 PCA3 0.705 <.001 0.647 <.001 PCDHGB7 0.712 <.001 PGF 0.790 0.039 PLG 0.764 0.048 PLP2 0.766 0.037 PPAP2B 0.589 <.001 0.647 <.001 0.691 <.001 0.765 0.013 PPP1R12A 0.673 0.001 0.677 0.001 0.807 0.045 PRIMA1 0.622 <.001 0.712 0.008 0.740 0.013 PRKCA 0.637 <.001 0.694 <.001 PRKCB 0.741 0.020 0.664 <.001 PROM1 0.599 0.017 0.527 0.042 0.610 0.006 0.420 0.002 PTCH1 0.752 0.027 0.762 0.011 PTEN 0.779 0.011 0.802 0.030 0.788 0.009 PTGS2 0.639 <.001 0.606 <.001 PTHLH 0.632 0.007 0.739 0.043 0.654 0.002 0.740 0.015 PTK2B 0.775 0.019 0.831 0.028 0.810 0.017 PTPN1 0.721 0.012 0.737 0.024 PYCARD 0.702 0.005 RAB27A 0.736 0.008 RAB30 0.761 0.011 RARB 0.746 0.010 RASSF1 0.805 0.043 RHOB 0.755 0.029 0.672 0.001 RLN1 0.742 0.036 0.740 0.036 RND3 0.607 <.001 0.633 <.001 RNF114 0.782 0.041 0.747 0.013 SDC2 0.714 0.002 SDHC 0.698 <.001 0.762 0.029 SERPINA3 0.752 0.030 SERPINB5 0.669 0.014 SH3RF2 0.705 0.012 0.568 <.001 0.755 0.016 SLC22A3 0.650 <.001 0.582 <.001 SMAD4 0.636 <.001 0.684 0.002 0.741 0.007 0.738 0.007 SMARCD1 0.757 0.001 SMO 0.790 0.049 0.766 0.013 SOD1 0.741 0.037 0.713 0.007 SORBS1 0.684 0.003 0.732 0.008 0.788 0.049 SPDEF 0.840 0.012 SPINT1 0.837 0.048 SRC 0.674 <.001 0.671 <.001 SRD5A2 0.553 <.001 0.588 <.001 0.618 <.001 0.701 <.001 ST5 0.747 0.012 0.761 0.010 0.780 0.016 0.832 0.041 STAT3 0.735 0.020 STAT5A 0.731 0.005 0.743 0.009 0.817 0.027 STAT5B 0.708 <.001 0.696 0.001 SUMO1 0.815 0.037 SVIL 0.689 0.003 0.739 0.008 0.761 0.011 TBP 0.792 0.037 TFF3 0.719 0.007 0.664 0.001 TGFB1I1 0.676 0.003 0.707 0.007 0.709 0.005 0.777 0.035 TGFB2 0.741 0.010 0.785 0.017 TGFBR2 0.759 0.022 TIMP3 0.785 0.037 TMPRSS2 0.780 0.012 0.742 <.001 TNF 0.654 0.007 0.682 0.006 TNFRSF10B 0.623 <.001 0.681 <.001 0.801 0.018 0.815 0.019 TNFSF10 0.721 0.004 TP53 0.759 0.011 TP63 0.737 0.020 0.754 0.007 TPM2 0.609 <.001 0.671 <.001 0.673 <.001 0.789 0.031 TRAF3IP2 0.795 0.041 0.727 0.005 TRO 0.793 0.033 0.768 0.027 0.814 0.023 TUBB2A 0.626 <.001 0.590 <.001 VCL 0.613 <.001 0.701 0.011 VIM 0.716 0.005 0.792 0.025 WFDC1 0.824 0.029 YY1 0.668 <.001 0.787 0.014 0.716 0.001 0.819 0.011 ZFHX3 0.732 <.001 0.709 <.001 ZFP36 0.656 0.001 0.609 <.001 0.818 0.045 ZNF827 0.750 0.022

Tables 6A and 6B provide genes that were significantly associated (p<0.05), positively or negatively, with recurrence (cRFI, bRFI) after adjusting for Gleason pattern in the primary and/or highest Gleason pattern. Increased expression of genes in Table 6A is negatively associated with good prognosis, while increased expression of gene in Table 6B is positively associated with good prognosis.

TABLE 6A Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern with a hazard ratio (HR) > 1.0 (increased expression is negatively associated with good prognosis) cRFI cRFI bRFI Primary Highest Primary bRFI Table 6A Pattern Pattern Pattern Highest Official p- p- p- Pattern Symbol HR value HR value HR value HR p-value AKR1C3 1.258 0.039 ANLN 1.292 0.023 1.449 <.001 1.420 0.001 AQP2 1.178 0.008 1.287 <.001 ASAP2 1.396 0.015 ASPN 1.809 <.001 1.508 0.009 1.506 0.002 1.438 0.002 BAG5 1.367 0.012 BAX 1.234 0.044 BGN 1.465 0.009 1.342 0.046 BIRC5 1.338 0.008 1.364 0.004 1.279 0.006 BMP6 1.369 0.015 1.518 0.002 BUB1 1.239 0.024 1.227 0.001 1.236 0.004 CACNA1D 1.337 0.025 CADPS 1.280 0.029 CCNE2 1.256 0.043 1.577 <.001 1.324 0.001 CD276 1.320 0.029 1.396 0.007 1.279 0.033 CDC20 1.298 0.016 1.334 0.002 1.257 0.032 1.279 0.003 CDH7 1.258 0.047 1.338 0.013 CDKN2B 1.342 0.032 1.488 0.009 CDKN2C 1.344 0.010 1.450 <.001 CDKN3 1.284 0.012 CENPF 1.289 0.048 1.498 0.001 1.344 0.010 COL1A1 1.481 0.003 1.506 0.002 COL3A1 1.459 0.004 1.430 0.013 COL4A1 1.396 0.015 COL8A1 1.413 0.008 CRISP3 1.346 0.012 1.310 0.025 CTHRC1 1.588 0.002 DDIT4 1.363 0.020 1.379 0.028 DICER1 1.294 0.008 ENY2 1.269 0.024 FADD 1.307 0.010 FAS 1.243 0.025 FGF5 1.328 0.002 GNPTAB 1.246 0.037 GREM1 1.332 0.024 1.377 0.013 1.373 0.011 HDAC1 1.301 0.018 1.237 0.021 HSD17B4 1.277 0.011 IFN-γ 1.219 0.048 IMMT 1.230 0.049 INHBA 1.866 <.001 1.944 <.001 JAG1 1.298 0.030 KCNN2 1.378 0.020 1.282 0.017 KHDRBS3 1.353 0.029 1.305 0.014 LAMA3 1.344 <.001 1.232 0.048 LAMC1 1.396 0.015 LIMS1 1.337 0.004 LOX 1.355 0.001 1.341 0.002 LTBP2 1.304 0.045 MAGEA4 1.215 0.024 MANF 1.460 <.001 MCM6 1.287 0.042 1.214 0.046 MELK 1.329 0.002 MMP11 1.281 0.050 MRPL13 1.266 0.021 MYBL2 1.453 <.001 1.274 0.019 MYC 1.265 0.037 MYO6 1.278 0.047 NETO2 1.322 0.022 NFKB1 1.255 0.032 NOX4 1.266 0.041 OR51E1 1.566 <.001 1.428 0.003 PATE1 1.242 <.001 1.347 <.001 1.177 0.011 PCNA 1.251 0.025 PEX10 1.302 0.028 PGD 1.335 0.045 1.379 0.014 1.274 0.025 PIM1 1.254 0.019 PLA2G7 1.289 0.025 1.250 0.031 PLAU 1.267 0.031 PSMD13 1.333 0.005 PTK6 1.432 <.001 1.577 <.001 1.223 0.040 PTTG1 1.279 0.013 1.308 0.006 RAGE 1.329 0.011 RALA 1.363 0.044 1.471 0.003 RGS7 1.120 0.040 1.173 0.031 RRM1 1.490 0.004 1.527 <.001 SESN3 1.353 0.017 SFRP4 1.370 0.025 SHMT2 1.460 0.008 1.410 0.006 1.407 0.008 1.345 <.001 SKIL 1.307 0.025 SLC25A21 1.414 0.002 1.330 0.004 SMARCC2 1.219 0.049 SPARC 1.431 0.005 TFDP1 1.283 0.046 1.345 0.003 THBS2 1.456 0.005 1.431 0.012 TK1 1.214 0.015 1.222 0.006 TOP2A 1.367 0.018 1.518 0.001 1.480 <.001 TPX2 1.513 0.001 1.607 <.001 1.588 <.001 1.481 <.001 UBE2T 1.409 0.002 1.285 0.018 UGT2B15 1.216 0.009 1.182 0.021 XIAP 1.336 0.037 1.194 0.043

TABLE 6B Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern with hazard ration (HR) < 1.0 (increased expression is positively associated with good prognosis) cRFI cRFI bRFI Primary Highest Primary bRFI Table 6B Pattern Pattern Pattern Highest Official p- p- p- Pattern Symbol HR value HR value HR value HR p-value AAMP 0.660 0.001 0.675 <.001 0.836 0.045 ABCA5 0.807 0.014 0.737 <.001 0.845 0.030 ABCC1 0.780 0.038 0.794 0.015 ABCG2 0.807 0.035 ABHD2 0.720 0.002 ADH5 0.750 0.034 AKAP1 0.721 <.001 ALDH1A2 0.735 0.009 0.592 <.001 0.756 0.007 0.781 0.021 ANGPT2 0.741 0.036 ANPEP 0.637 <.001 0.536 <.001 ANXA2 0.762 0.044 APOE 0.707 0.013 APRT 0.727 0.004 0.771 0.006 ATXN1 0.725 0.013 AURKA 0.784 0.037 0.735 0.003 AXIN2 0.744 0.004 0.630 <.001 AZGP1 0.672 <.001 0.720 <.001 0.764 0.001 BAD 0.687 <.001 BAK1 0.783 0.014 BCL2 0.777 0.033 0.772 0.036 BIK 0.768 0.040 BIN1 0.691 <.001 BTRC 0.776 0.029 C7 0.707 0.004 0.791 0.024 CADM1 0.587 <.001 0.593 <.001 CASP1 0.773 0.023 0.820 0.025 CAV1 0.753 0.014 CAV2 0.627 0.009 0.682 0.003 CCL2 0.740 0.019 CCNH 0.736 0.003 CCR1 0.755 0.022 CD1A 0.740 0.025 CD44 0.590 <.001 0.637 <.001 CD68 0.757 0.026 CD82 0.778 0.012 0.759 0.016 CDC25B 0.760 0.021 CDK3 0.762 0.024 0.774 0.007 CDKN1A 0.714 0.015 CDKN1C 0.738 0.014 0.768 0.021 COL6A1 0.690 <.001 0.805 0.048 CSF1 0.675 0.002 0.779 0.036 CSK 0.825 0.004 CTNNB1 0.884 0.045 0.888 0.027 CTSB 0.740 0.017 0.676 0.003 0.755 0.010 CTSD 0.673 0.031 0.722 0.009 CTSK 0.804 0.034 CTSL2 0.748 0.019 CXCL12 0.731 0.017 CYP3A5 0.523 <.001 0.518 <.001 CYR61 0.744 0.041 DAP 0.755 0.011 DARC 0.763 0.029 DDR2 0.813 0.041 DES 0.743 0.020 DHRS9 0.606 0.001 DHX9 0.916 0.021 DIAPH1 0.749 0.036 0.688 0.003 DLGAP1 0.758 0.042 0.676 0.002 DLL4 0.779 0.010 DNM3 0.732 0.007 DPP4 0.732 0.004 0.750 0.014 DPT 0.704 0.014 DUSP6 0.662 <.001 0.665 0.001 EBNA1BP2 0.828 0.019 EDNRA 0.782 0.048 EGF 0.712 0.023 EGR1 0.678 0.004 0.725 0.028 EGR3 0.680 0.006 0.738 0.027 EIF2C2 0.789 0.032 EIF2S3 0.759 0.012 ELK4 0.745 0.024 EPHA2 0.661 0.007 EPHA3 0.781 0.026 0.828 0.037 ERBB2 0.791 0.022 0.760 0.014 0.789 0.006 ERBB3 0.757 0.009 ERCC1 0.760 0.008 ESR1 0.742 0.014 ESR2 0.711 0.038 ETV4 0.714 0.035 FAM107A 0.619 <.001 0.710 0.011 0.781 0.019 FAM13C 0.664 <.001 0.686 <.001 0.813 0.014 FAM49B 0.670 <.001 0.793 0.014 0.815 0.044 0.843 0.047 FASLG 0.616 0.004 0.813 0.038 FGF10 0.751 0.028 0.766 0.019 FGF17 0.718 0.031 0.765 0.019 FGFR2 0.740 0.009 0.738 0.002 FKBP5 0.749 0.031 FLNC 0.826 0.029 FLT1 0.779 0.045 0.729 0.006 FLT4 0.815 0.024 FOS 0.657 0.003 0.656 0.004 FSD1 0.763 0.017 FYN 0.716 0.004 0.792 0.024 GADD45B 0.692 0.009 0.697 0.010 GDF15 0.767 0.016 GHR 0.701 0.002 0.704 0.002 0.640 <.001 GNRH1 0.778 0.039 GPM6B 0.749 0.010 0.750 0.010 0.827 0.037 GRB7 0.696 0.005 GSK3B 0.726 0.005 GSN 0.660 <.001 0.752 0.019 GSTM1 0.710 0.004 0.676 <.001 GSTM2 0.643 <.001 0.767 0.015 HK1 0.798 0.035 HLA-G 0.660 0.013 HLF 0.644 <.001 0.727 0.011 HNF1B 0.755 0.013 HPS1 0.756 0.006 0.791 0.043 HSD17B10 0.737 0.006 HSD3B2 0.674 0.003 HSP90AB1 0.763 0.015 HSPB1 0.787 0.020 0.778 0.015 HSPE1 0.794 0.039 ICAM1 0.664 0.003 IER3 0.699 0.003 0.693 0.010 IFIT1 0.621 <.001 0.733 0.027 IGF1 0.751 0.017 0.655 <.001 IGFBP2 0.599 <.001 0.605 <.001 IGFBP5 0.745 0.007 0.775 0.035 IGFBP6 0.671 0.005 IL1B 0.732 0.016 0.717 0.005 IL6 0.763 0.040 IL6R 0.764 0.022 IL6ST 0.647 <.001 0.739 0.012 IL8 0.711 0.015 0.694 0.006 ING5 0.729 0.007 0.727 0.003 ITGA4 0.755 0.009 ITGA5 0.743 0.018 0.770 0.034 ITGA6 0.816 0.044 0.772 0.006 ITGA7 0.680 0.004 ITGAD 0.590 0.009 ITGB4 0.663 <.001 0.658 <.001 0.759 0.004 JUN 0.656 0.004 0.639 0.003 KIAA0196 0.737 0.011 KIT 0.730 0.021 0.724 0.008 KLC1 0.755 0.035 KLK1 0.706 0.008 KLK2 0.740 0.016 0.723 0.001 KLK3 0.765 0.006 0.740 0.002 KRT1 0.774 0.042 KRT15 0.658 <.001 0.632 <.001 0.764 0.008 KRT18 0.703 0.004 0.672 <.001 0.779 0.015 0.811 0.032 KRT5 0.686 <.001 0.629 <.001 0.802 0.023 KRT8 0.763 0.034 0.771 0.022 L1CAM 0.748 0.041 LAG3 0.693 0.008 0.724 0.020 LAMA4 0.689 0.039 LAMB3 0.667 <.001 0.645 <.001 0.773 0.006 LGALS3 0.666 <.001 0.822 0.047 LIG3 0.723 0.008 LRP1 0.777 0.041 0.769 0.007 MDM2 0.688 <.001 MET 0.709 0.010 0.736 0.028 0.715 0.003 MGMT 0.751 0.031 MICA 0.705 0.002 MPPED2 0.690 0.001 0.657 <.001 0.708 <.001 MRC1 0.812 0.049 MSH6 0.860 0.049 MTSS1 0.686 0.001 MVP 0.798 0.034 0.761 0.033 MYBPC1 0.754 0.009 0.615 <.001 NCAPD3 0.739 0.021 0.664 0.005 NEXN 0.798 0.037 NFAT5 0.596 <.001 0.732 0.005 NFATC2 0.743 0.016 0.792 0.047 NOS3 0.730 0.012 0.757 0.032 OAZ1 0.732 0.020 0.705 0.002 OCLN 0.746 0.043 0.784 0.025 OLFML3 0.711 0.002 0.709 <.001 0.720 0.001 OMD 0.729 0.011 0.762 0.033 OSM 0.813 0.028 PAGE4 0.668 0.003 0.725 0.004 0.688 <.001 0.766 0.005 PCA3 0.736 0.001 0.691 <.001 PCDHGB7 0.769 0.019 0.789 0.022 PIK3CA 0.768 0.010 PIK3CG 0.792 0.019 0.758 0.009 PLG 0.682 0.009 PPAP2B 0.688 0.005 0.815 0.046 PPP1R12A 0.731 0.026 0.775 0.042 PRIMA1 0.697 0.004 0.757 0.032 PRKCA 0.743 0.019 PRKCB 0.756 0.036 0.767 0.029 PROM1 0.640 0.027 0.699 0.034 0.503 0.013 PTCH1 0.730 0.018 PTEN 0.779 0.015 0.789 0.007 PTGS2 0.644 <.001 0.703 0.007 PTHLH 0.655 0.012 0.706 0.038 0.634 0.001 0.665 0.003 PTK2B 0.779 0.023 0.702 0.002 0.806 0.015 0.806 0.024 PYCARD 0.659 0.001 RAB30 0.779 0.033 0.754 0.014 RARB 0.787 0.043 0.742 0.009 RASSF1 0.754 0.005 RHOA 0.796 0.041 0.819 0.048 RND3 0.721 0.011 0.743 0.028 SDC1 0.707 0.011 SDC2 0.745 0.002 SDHC 0.750 0.013 SERPINA3 0.730 0.016 SERPINB5 0.715 0.041 SH3RF2 0.698 0.025 SIPA1L1 0.796 0.014 0.820 0.004 SLC22A3 0.724 0.014 0.700 0.008 SMAD4 0.668 0.002 0.771 0.016 SMARCD1 0.726 <.001 0.700 0.001 0.812 0.028 SMO 0.785 0.027 SOD1 0.735 0.012 SORBS1 0.785 0.039 SPDEF 0.818 0.002 SPINT1 0.761 0.024 0.773 0.006 SRC 0.709 <.001 0.690 <.001 SRD5A1 0.746 0.010 0.767 0.024 0.745 0.003 SRD5A2 0.575 <.001 0.669 0.001 0.674 <.001 0.781 0.018 ST5 0.774 0.027 STAT1 0.694 0.004 STAT5A 0.719 0.004 0.765 0.006 0.834 0.049 STAT5B 0.704 0.001 0.744 0.012 SUMO1 0.777 0.014 SVIL 0.771 0.026 TBP 0.774 0.031 TFF3 0.742 0.015 0.719 0.024 TGFB1I1 0.763 0.048 TGFB2 0.729 0.011 0.758 0.002 TMPRSS2 0.810 0.034 0.692 <.001 TNF 0.727 0.022 TNFRSF10A 0.805 0.025 TNFRSF10B 0.581 <.001 0.738 0.014 0.809 0.034 TNFSF10 0.751 0.015 0.700 <.001 TP63 0.723 0.018 0.736 0.003 TPM2 0.708 0.010 0.734 0.014 TRAF3IP2 0.718 0.004 TRO 0.742 0.012 TSTA3 0.774 0.028 TUBB2A 0.659 <.001 0.650 <.001 TYMP 0.695 0.002 VCL 0.683 0.008 VIM 0.778 0.040 WDR19 0.775 0.014 XRCC5 0.793 0.042 YY1 0.751 0.025 0.810 0.008 ZFHX3 0.760 0.005 0.726 0.001 ZFP36 0.707 0.008 0.672 0.003 ZNF827 0.667 0.002 0.792 0.039

Tables 7A and 7B provide genes significantly associated (p<0.05), positively or negatively, with clinical recurrence (cRFI) in negative TMPRSS fusion specimens in the primary or highest Gleason pattern specimen. Increased expression of genes in Table 7A is negatively associated with good prognosis, while increased expression of genes in Table 7B is positively associated with good prognosis.

TABLE 7A Genes significantly (p < 0.05) associated with cRFI for TMPRSS2- ERG fusion negative in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) >1.0 (increased expression is negatively associated with good prognosis) Table 7A Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value ANLN 1.42 0.012 1.36 0.004 AQP2 1.25 0.033 ASPN 2.48 <.001 1.65 <.001 BGN 2.04 <.001 1.45 0.007 BIRC5 1.59 <.001 1.37 0.005 BMP6 1.95 <.001 1.43 0.012 BMPR1B 1.93 0.002 BUB1 1.51 <.001 1.35 <.001 CCNE2 1.48 0.007 CD276 1.93 <.001 1.79 <.001 CDC20 1.49 0.004 1.47 <.001 CDC6 1.52 0.009 1.34 0.022 CDKN2B 1.54 0.008 1.55 0.003 CDKN2C 1.55 0.003 1.57 <.001 CDKN3 1.34 0.026 CENPF 1.63 0.002 1.33 0.018 CKS2 1.50 0.026 1.43 0.009 CLTC 1.46 0.014 COL1A1 1.98 <.001 1.50 0.002 COL3A1 2.03 <.001 1.42 0.007 COL4A1 1.81 0.002 COL8A1 1.63 0.004 1.60 0.001 CRISP3 1.31 0.016 CTHRC1 1.67 0.006 1.48 0.005 DDIT4 1.49 0.037 ENY2 1.29 0.039 EZH2 1.35 0.016 F2R 1.46 0.034 1.46 0.007 FAP 1.66 0.006 1.38 0.012 FGF5 1.46 0.001 GNPTAB 1.49 0.013 HSD17B4 1.34 0.039 1.44 0.002 INHBA 2.92 <.001 2.19 <.001 JAG1 1.38 0.042 KCNN2 1.71 0.002 1.73 <.001 KHDRBS3 1.46 0.015 KLK14 1.28 0.034 KPNA2 1.63 0.016 LAMC1 1.41 0.044 LOX 1.29 0.036 LTBP2 1.57 0.017 MELK 1.38 0.029 MMP11 1.69 0.002 1.42 0.004 MYBL2 1.78 <.001 1.49 <.001 NETO2 2.01 <.001 1.43 0.007 NME1 1.38 0.017 PATE1 1.43 <.001 1.24 0.005 PEX10 1.46 0.030 PGD 1.77 0.002 POSTN 1.49 0.037 1.34 0.026 PPFIA3 1.51 0.012 PPP3CA 1.46 0.033 1.34 0.020 PTK6 1.69 <.001 1.56 <.001 PTTG1 1.35 0.028 RAD51 1.32 0.048 RALBP1 1.29 0.042 RGS7 1.18 0.012 1.32 0.009 RRM1 1.57 0.016 1.32 0.041 RRM2 1.30 0.039 SAT1 1.61 0.007 SESN3 1.76 <.001 1.36 0.020 SFRP4 1.55 0.016 1.48 0.002 SHMT2 2.23 <.001 1.59 <.001 SPARC 1.54 0.014 SQLE 1.86 0.003 STMN1 2.14 <.001 THBS2 1.79 <.001 1.43 0.009 TK1 1.30 0.026 TOP2A 2.03 <.001 1.47 0.003 TPD52 1.63 0.003 TPX2 2.11 <.001 1.63 <.001 TRAP1 1.46 0.023 UBE2C 1.57 <.001 1.58 <.001 UBE2G1 1.56 0.008 UBE2T 1.75 <.001 UGT2B15 1.31 0.036 1.33 0.004 UHRF1 1.46 0.007 UTP23 1.52 0.017

TABLE 7B Genes significantly (p < 0.05) associated with cRFI for TMPRSS2- ERG fusion negative in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) <1.0 (increased expression is positively associated with good prognosis) Table 7B Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value AAMP 0.56 <.001 0.65 0.001 ABCA5 0.64 <.001 0.71 <.001 ABCB1 0.62 0.004 ABCC3 0.74 0.031 ABCG2 0.78 0.050 ABHD2 0.71 0.035 ACOX2 0.54 <.001 0.71 0.007 ADH5 0.49 <.001 0.61 <.001 AKAP1 0.77 0.031 0.76 0.013 AKR1C1 0.65 0.006 0.78 0.044 AKT1 0.72 0.020 AKT3 0.75 <.001 ALDH1A2 0.53 <.001 0.60 <.001 AMPD3 0.62 <.001 0.78 0.028 ANPEP 0.54 <.001 0.61 <.001 ANXA2 0.63 0.008 0.74 0.016 ARHGAP29 0.67 0.005 0.77 0.016 ARHGDIB 0.64 0.013 ATP5J 0.57 0.050 ATXN1 0.61 0.004 0.77 0.043 AXIN2 0.51 <.001 0.62 <.001 AZGP1 0.61 <.001 0.64 <.001 BCL2 0.64 0.004 0.75 0.029 BIN1 0.52 <.001 0.74 0.010 BTG3 0.75 0.032 0.75 0.010 BTRC 0.69 0.011 C7 0.51 <.001 0.67 <.001 CADM1 0.49 <.001 0.76 0.034 CASP1 0.71 0.010 0.74 0.007 CAV1 0.73 0.015 CCL5 0.67 0.018 0.67 0.003 CCNH 0.63 <.001 0.75 0.004 CCR1 0.77 0.032 CD164 0.52 <.001 0.63 <.001 CD44 0.53 <.001 0.74 0.014 CDH10 0.69 0.040 CDH18 0.40 0.011 CDK14 0.75 0.013 CDK2 0.81 0.031 CDK3 0.73 0.022 CDKN1A 0.68 0.038 CDKN1C 0.62 0.003 0.72 0.005 COL6A1 0.54 <.001 0.70 0.004 COL6A3 0.64 0.004 CSF1 0.56 <.001 0.78 0.047 CSRP1 0.40 <.001 0.66 0.002 CTGF 0.66 0.015 0.74 0.027 CTNNB1 0.69 0.043 CTSB 0.60 0.002 0.71 0.011 CTSS 0.67 0.013 CXCL12 0.56 <.001 0.77 0.026 CYP3A5 0.43 <.001 0.63 <.001 CYR61 0.43 <.001 0.58 <.001 DAG1 0.72 0.012 DARC 0.66 0.016 DDR2 0.65 0.007 DES 0.52 <.001 0.74 0.018 DHRS9 0.54 0.007 DICER1 0.70 0.044 DLC1 0.75 0.021 DLGAP1 0.55 <.001 0.72 0.005 DNM3 0.61 0.001 DPP4 0.55 <.001 0.77 0.024 DPT 0.48 <.001 0.61 <.001 DUSP1 0.47 <.001 0.59 <.001 DUSP6 0.65 0.009 0.65 0.002 DYNLL1 0.74 0.045 EDNRA 0.61 0.002 0.75 0.038 EFNB2 0.71 0.043 EGR1 0.43 <.001 0.58 <.001 EGR3 0.47 <.001 0.66 <.001 EIF5 0.77 0.028 ELK4 0.49 <.001 0.72 0.012 EPHA2 0.70 0.007 EPHA3 0.62 <.001 0.72 0.009 EPHB2 0.68 0.009 ERBB2 0.64 <.001 0.63 <.001 ERBB3 0.69 0.018 ERCC1 0.69 0.019 0.77 0.021 ESR2 0.61 0.020 FAAH 0.57 <.001 0.77 0.035 FABP5 0.67 0.035 FAM107A 0.42 <.001 0.59 <.001 FAM13C 0.53 <.001 0.59 <.001 FAS 0.71 0.035 FASLG 0.56 0.017 0.67 0.014 FGF10 0.57 0.002 FGF17 0.70 0.039 0.70 0.010 FGF7 0.63 0.005 0.70 0.004 FGFR2 0.63 0.003 0.71 0.003 FKBP5 0.72 0.020 FLNA 0.48 <.001 0.74 0.022 FOS 0.45 <.001 0.56 <.001 FOXO1 0.59 <.001 FOXQ1 0.57 <.001 0.69 0.008 FYN 0.62 0.001 0.74 0.013 G6PD 0.77 0.014 GADD45A 0.73 0.045 GADD45B 0.45 <.001 0.64 0.001 GDF15 0.58 <.001 GHR 0.62 0.008 0.68 0.002 GPM6B 0.60 <.001 0.70 0.003 GSK3B 0.71 0.016 0.71 0.006 GSN 0.46 <.001 0.66 <.001 GSTM1 0.56 <.001 0.62 <.001 GSTM2 0.47 <.001 0.67 <.001 HGD 0.72 0.002 HIRIP3 0.69 0.021 0.69 0.002 HK1 0.68 0.005 0.73 0.005 HLA-G 0.54 0.024 0.65 0.013 HLF 0.41 <.001 0.68 0.001 HNF1B 0.55 <.001 0.59 <.001 HPS1 0.74 0.015 0.76 0.025 HSD17B3 0.65 0.031 HSPB2 0.62 0.004 0.76 0.027 ICAM1 0.61 0.010 IER3 0.55 <.001 0.67 0.003 IFIT1 0.57 <.001 0.70 0.008 IFNG 0.69 0.040 IGF1 0.63 <.001 0.59 <.001 IGF2 0.67 0.019 0.70 0.005 IGFBP2 0.53 <.001 0.63 <.001 IGFBP5 0.57 <.001 0.71 0.006 IGFBP6 0.41 <.001 0.71 0.012 IL10 0.59 0.020 IL1B 0.53 <.001 0.70 0.005 IL6 0.55 0.001 IL6ST 0.45 <.001 0.68 <.001 IL8 0.60 0.005 0.70 0.008 ILK 0.68 0.029 0.76 0.036 ING5 0.54 <.001 0.82 0.033 ITGA1 0.66 0.017 ITGA3 0.70 0.020 ITGA5 0.64 0.011 ITGA6 0.66 0.003 0.74 0.006 ITGA7 0.50 <.001 0.71 0.010 ITGB4 0.63 0.014 0.73 0.010 ITPR1 0.55 <.001 ITPR3 0.76 0.007 JUN 0.37 <.001 0.54 <.001 JUNB 0.58 0.002 0.71 0.016 KCTD12 0.68 0.017 KIT 0.49 0.002 0.76 0.043 KLC1 0.61 0.005 0.77 0.045 KLF6 0.65 0.009 KLK1 0.68 0.036 KLK10 0.76 0.037 KLK2 0.64 <.001 0.73 0.006 KLK3 0.65 <.001 0.76 0.021 KLRK1 0.63 0.005 KRT15 0.52 <.001 0.58 <.001 KRT18 0.46 <.001 KRT5 0.51 <.001 0.58 <.001 KRT8 0.53 <.001 L1CAM 0.65 0.031 LAG3 0.58 0.002 0.76 0.033 LAMA4 0.52 0.018 LAMB3 0.60 0.002 0.65 0.003 LGALS3 0.52 <.001 0.71 0.002 LIG3 0.65 0.011 LRP1 0.61 0.001 0.75 0.040 MGMT 0.66 0.003 MICA 0.59 0.001 0.68 0.001 MLXIP 0.70 0.020 MMP2 0.68 0.022 MMP9 0.67 0.036 MPPED2 0.57 <.001 0.66 <.001 MRC1 0.69 0.028 MTSS1 0.63 0.005 0.79 0.037 MVP 0.62 <.001 MYBPC1 0.53 <.001 0.70 0.011 NCAM1 0.70 0.039 0.77 0.042 NCAPD3 0.52 <.001 0.59 <.001 NDRG1 0.69 0.008 NEXN 0.62 0.002 NFAT5 0.45 <.001 0.59 <.001 NFATC2 0.68 0.035 0.75 0.036 NFKBIA 0.70 0.030 NRG1 0.59 0.022 0.71 0.018 OAZ1 0.69 0.018 0.62 <.001 OLFML3 0.59 <.001 0.72 0.003 OR51E2 0.73 0.013 PAGE4 0.42 <.001 0.62 <.001 PCA3 0.53 <.001 PCDHGB7 0.70 0.032 PGF 0.68 0.027 0.71 0.013 PGR 0.76 0.041 PIK3C2A 0.80 <.001 PIK3CA 0.61 <.001 0.80 0.036 PIK3CG 0.67 0.001 0.76 0.018 PLP2 0.65 0.015 0.72 0.010 PPAP2B 0.45 <.001 0.69 0.003 PPP1R12A 0.61 0.007 0.73 0.017 PRIMA1 0.51 <.001 0.68 0.004 PRKCA 0.55 <.001 0.74 0.009 PRKCB 0.55 <.001 PROM1 0.67 0.042 PROS1 0.73 0.036 PTCH1 0.69 0.024 0.72 0.010 PTEN 0.54 <.001 0.64 <.001 PTGS2 0.48 <.001 0.55 <.001 PTH1R 0.57 0.003 0.77 0.050 PTHLH 0.55 0.010 PTK2B 0.56 <.001 0.70 0.001 PYCARD 0.73 0.009 RAB27A 0.65 0.009 0.71 0.014 RAB30 0.59 0.003 0.72 0.010 RAGE 0.76 0.011 RARB 0.59 <.001 0.63 <.001 RASSF1 0.67 0.003 RB1 0.67 0.006 RFX1 0.71 0.040 0.70 0.003 RHOA 0.71 0.038 0.65 <.001 RHOB 0.58 0.001 0.71 0.006 RND3 0.54 <.001 0.69 0.003 RNF114 0.59 0.004 0.68 0.003 SCUBE2 0.77 0.046 SDHC 0.72 0.028 0.76 0.025 SEC23A 0.75 0.029 SEMA3A 0.61 0.004 0.72 0.011 SEPT9 0.66 0.013 0.76 0.036 SERPINB5 0.75 0.039 SH3RF2 0.44 <.001 0.48 <.001 SHH 0.74 0.049 SLC22A3 0.42 <.001 0.61 <.001 SMAD4 0.45 <.001 0.66 <.001 SMARCD1 0.69 0.016 SOD1 0.68 0.042 SORBS1 0.51 <.001 0.73 0.012 SPARCL1 0.58 <.001 0.77 0.040 SPDEF 0.77 <.001 SPINT1 0.65 0.004 0.79 0.038 SRC 0.61 <.001 0.69 0.001 SRD5A2 0.39 <.001 0.55 <.001 ST5 0.61 <.001 0.73 0.012 STAT1 0.64 0.006 STAT3 0.63 0.010 STAT5A 0.62 0.001 0.70 0.003 STAT5B 0.58 <.001 0.73 0.009 SUMO1 0.66 <.001 SVIL 0.57 0.001 0.74 0.022 TBP 0.65 0.002 TFF1 0.65 0.021 TFF3 0.58 <.001 TGFB1I1 0.51 <.001 0.75 0.026 TGFB2 0.48 <.001 0.62 <.001 TGFBR2 0.61 0.003 TIAM1 0.68 0.019 TIMP2 0.69 0.020 TIMP3 0.58 0.002 TNFRSF10A 0.73 0.047 TNFRSF10B 0.47 <.001 0.70 0.003 TNFSF10 0.56 0.001 TP63 0.67 0.001 TPM1 0.58 0.004 0.73 0.017 TPM2 0.46 <.001 0.70 0.005 TRA2A 0.68 0.013 TRAF3IP2 0.73 0.041 0.71 0.004 TRO 0.72 0.016 0.71 0.004 TUBB2A 0.53 <.001 0.73 0.021 TYMP 0.70 0.011 VCAM1 0.69 0.041 VCL 0.46 <.001 VEGFA 0.77 0.039 VEGFB 0.71 0.035 VIM 0.60 0.001 XRCC5 0.75 0.026 YY1 0.62 0.008 0.77 0.039 ZFHX3 0.53 <.001 0.58 <.001 ZFP36 0.43 <.001 0.54 <.001 ZNF827 0.55 0.001

Tables 8A and 8B provide genes that were significantly associated (p<0.05), positively or negatively, with clinical recurrence (cRFI) in positive TMPRSS fusion specimens in the primary or highest Gleason pattern specimen. Increased expression of genes in Table 8A is negatively associated with good prognosis, while increased expression of genes in Table 8B is positively associated with good prognosis.

TABLE 8A Genes significantly (p < 0.05) associated with cRFI for TMPRSS2- ERG fusion positive in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) >1.0 (increased expression is negatively associated with good prognosis) Table 8A Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value ACTR2 1.78 0.017 AKR1C3 1.44 0.013 ALCAM 1.44 0.022 ANLN 1.37 0.046 1.81 <.001 APOE 1.49 0.023 1.66 0.005 AQP2 1.30 0.013 ARHGDIB 1.55 0.021 ASPN 2.13 <.001 2.43 <.001 ATP5E 1.69 0.013 1.58 0.014 BGN 1.92 <.001 2.55 <.001 BIRC5 1.48 0.006 1.89 <.001 BMP6 1.51 0.010 1.96 <.001 BRCA2 1.41 0.007 BUB1 1.36 0.007 1.52 <.001 CCNE2 1.55 0.004 1.59 <.001 CD276 1.65 <.001 CDC20 1.68 <.001 1.74 <.001 CDH11 1.50 0.017 CDH18 1.36 <.001 CDH7 1.54 0.009 1.46 0.026 CDKN2B 1.68 0.008 1.93 0.001 CDKN2C 2.01 <.001 1.77 <.001 CDKN3 1.51 0.002 1.33 0.049 CENPF 1.51 0.007 2.04 <.001 CKS2 1.43 0.034 1.56 0.007 COL1A1 2.23 <.001 3.04 <.001 COL1A2 1.79 0.001 2.22 <.001 COL3A1 1.96 <.001 2.81 <.001 COL4A1 1.52 0.020 COL5A1 1.50 0.020 COL5A2 1.64 0.017 1.55 0.010 COL8A1 1.96 <.001 2.38 <.001 CRISP3 1.68 0.002 1.67 0.002 CTHRC1 2.06 <.001 CTNND2 1.42 0.046 1.50 0.025 CTSK 1.43 0.049 CXCR4 1.82 0.001 1.64 0.007 DDIT4 1.54 0.016 1.58 0.009 DLL4 1.51 0.007 DYNLL1 1.50 0.021 1.22 0.002 F2R 2.27 <.001 2.02 <.001 FAP 2.12 <.001 FCGR3A 1.94 0.002 FGF5 1.23 0.047 FOXP3 1.52 0.006 1.48 0.018 GNPTAB 1.44 0.042 GPR68 1.51 0.011 GREM1 1.91 <.001 2.38 <.001 HDAC1 1.43 0.048 HDAC9 1.65 <.001 1.67 0.004 HRAS 1.65 0.005 1.58 0.021 IGFBP3 1.94 <.001 1.85 <.001 INHBA 2.03 <.001 2.64 <.001 JAG1 1.41 0.027 1.50 0.008 KCTD12 1.51 0.017 KHDRBS3 1.48 0.029 1.54 0.014 KPNA2 1.46 0.050 LAMA3 1.35 0.040 LAMC1 1.77 0.012 LTBP2 1.82 <.001 LUM 1.51 0.021 1.53 0.009 MELK 1.38 0.020 1.49 0.001 MKI67 1.37 0.014 MMP11 1.73 <.001 1.69 <.001 MRPL13 1.30 0.046 MYBL2 1.56 <.001 1.72 <.001 MYLK3 1.17 0.007 NOX4 1.58 0.005 1.96 <.001 NRIP3 1.30 0.040 NRP1 1.53 0.021 OLFML2B 1.54 0.024 OSM 1.43 0.018 PATE1 1.20 <.001 1.33 <.001 PCNA 1.64 0.003 PEX10 1.41 0.041 1.64 0.003 PIK3CA 1.38 0.037 PLK1 1.52 0.009 1.67 0.002 PLOD2 1.65 0.002 POSTN 1.79 <.001 2.06 <.001 PTK6 1.67 0.002 2.38 <.001 PTTG1 1.56 0.002 1.54 0.003 RAD21 1.61 0.036 1.53 0.005 RAD51 1.33 0.009 RALA 1.95 0.004 1.60 0.007 REG4 1.43 0.042 ROBO2 1.46 0.024 RRM1 1.44 0.033 RRM2 1.50 0.003 1.48 <.001 SAT1 1.42 0.009 1.43 0.012 SEC14L1 1.64 0.002 SFRP4 2.07 <.001 2.40 <.001 SHMT2 1.52 0.030 1.60 0.001 SLC44A1 1.42 0.039 SPARC 1.93 <.001 2.21 <.001 SULF1 1.63 0.006 2.04 <.001 THBS2 1.95 <.001 2.26 <.001 THY1 1.69 0.016 1.95 0.002 TK1 1.43 0.003 TOP2A 1.57 0.002 2.11 <.001 TPX2 1.84 <.001 2.27 <.001 UBE2C 1.41 0.011 1.44 0.006 UBE2T 1.63 0.001 UHRF1 1.51 0.007 1.69 <.001 WISP1 1.47 0.045 WNT5A 1.35 0.027 1.63 0.001 ZWINT 1.36 0.045

TABLE 8B Genes significantly (p < 0.05) associated with cRFI for TMPRSS2- ERG fusion positive in the primary Gleason pattern or highest Gleason pattern with hazard ratio (HR) <1.0 (increased expression is positively associated with good prognosis) Table 8B Primary Pattern Highest Pattern Official Symbol HR p-value HR p-value AAMP 0.57 0.007 0.58 <.001 ABCA5 0.80 0.044 ACE 0.65 0.023 0.55 <.001 ACOX2 0.55 <.001 ADH5 0.68 0.022 AKAP1 0.81 0.043 ALDH1A2 0.72 0.036 0.43 <.001 ANPEP 0.66 0.022 0.46 <.001 APRT 0.73 0.040 AXIN2 0.60 <.001 AZGP1 0.57 <.001 0.65 <.001 BCL2 0.69 0.035 BIK 0.71 0.045 BIN1 0.71 0.004 0.71 0.009 BTRC 0.66 0.003 0.58 <.001 C7 0.64 0.006 CADM1 0.61 <.001 0.47 <.001 CCL2 0.73 0.042 CCNH 0.69 0.022 CD44 0.56 <.001 0.58 <.001 CD82 0.72 0.033 CDC25B 0.74 0.028 CDH1 0.75 0.030 0.72 0.010 CDH19 0.56 0.015 CDK3 0.78 0.045 CDKN1C 0.74 0.045 0.70 0.014 CSF1 0.72 0.037 CTSB 0.69 0.048 CTSL2 0.58 0.005 CYP3A5 0.51 <.001 0.30 <.001 DHX9 0.89 0.006 0.87 0.012 DLC1 0.64 0.023 DLGAP1 0.69 0.010 0.49 <.001 DPP4 0.64 <.001 0.56 <.001 DPT 0.63 0.003 EGR1 0.69 0.035 EGR3 0.68 0.025 EIF2S3 0.70 0.021 EIF5 0.71 0.030 ELK4 0.71 0.041 0.60 0.003 EPHA2 0.72 0.036 0.66 0.011 EPHB4 0.65 0.007 ERCC1 0.68 0.023 ESR2 0.64 0.027 FAM107A 0.64 0.003 0.61 0.003 FAM13C 0.68 0.006 0.55 <.001 FGFR2 0.73 0.033 0.59 <.001 FKBP5 0.60 0.006 FLNC 0.68 0.024 0.65 0.012 FLT1 0.71 0.027 FOS 0.62 0.006 FOXO1 0.75 0.010 GADD45B 0.68 0.020 GHR 0.62 0.006 GPM6B 0.57 <.001 GSTM1 0.68 0.015 0.58 <.001 GSTM2 0.65 0.005 0.47 <.001 HGD 0.63 0.001 0.71 0.020 HK1 0.67 0.003 0.62 0.002 HLF 0.59 <.001 HNF1B 0.66 0.004 0.61 0.001 IER3 0.70 0.026 IGF1 0.63 0.005 0.55 <.001 IGF1R 0.76 0.049 IGFBP2 0.59 0.007 0.64 0.003 IL6ST 0.65 0.005 IL8 0.61 0.005 0.66 0.019 ILK 0.64 0.015 ING5 0.73 0.033 0.70 0.009 ITGA7 0.72 0.045 0.69 0.019 ITGB4 0.63 0.002 KLC1 0.74 0.045 KLK1 0.56 0.002 0.49 <.001 KLK10 0.68 0.013 KLK11 0.66 0.003 KLK2 0.66 0.045 0.65 0.011 KLK3 0.75 0.048 0.77 0.014 KRT15 0.71 0.017 0.50 <.001 KRT5 0.73 0.031 0.54 <.001 LAMA5 0.70 0.044 LAMB3 0.70 0.005 0.58 <.001 LGALS3 0.69 0.025 LIG3 0.68 0.022 MDK 0.69 0.035 MGMT 0.59 0.017 0.60 <.001 MGST1 0.73 0.042 MICA 0.70 0.009 MPPED2 0.72 0.031 0.54 <.001 MTSS1 0.62 0.003 MYBPC1 0.50 <.001 NCAPD3 0.62 0.007 0.38 <.001 NCOR1 0.82 0.048 NFAT5 0.60 0.001 0.62 <.001 NRG1 0.66 0.040 0.61 0.029 NUP62 0.75 0.037 OMD 0.54 <.001 PAGE4 0.64 0.005 PCA3 0.66 0.012 PCDHGB7 0.68 0.018 PGR 0.60 0.012 PPAP2B 0.62 0.010 PPP1R12A 0.73 0.031 0.58 0.003 PRIMA1 0.65 0.013 PROM1 0.41 0.013 PTCH1 0.64 0.006 PTEN 0.75 0.047 PTGS2 0.67 0.011 PTK2B 0.66 0.005 PTPN1 0.71 0.026 RAGE 0.70 0.012 RARB 0.68 0.016 RGS10 0.84 0.034 RHOB 0.66 0.016 RND3 0.63 0.004 SDHC 0.73 0.044 0.69 0.016 SERPINA3 0.67 0.011 0.51 <.001 SERPINB5 0.42 <.001 SH3RF2 0.66 0.012 0.51 <.001 SLC22A3 0.59 0.003 0.48 <.001 SMAD4 0.64 0.004 0.49 <.001 SMARCC2 0.73 0.042 SMARCD1 0.73 <.001 0.76 0.035 SMO 0.64 0.006 SNAI1 0.53 0.008 SOD1 0.60 0.003 SRC 0.64 <.001 0.61 <.001 SRD5A2 0.63 0.004 0.59 <.001 STAT3 0.64 0.014 STAT5A 0.70 0.032 STAT5B 0.74 0.034 0.63 0.003 SVIL 0.71 0.028 TGFB1I1 0.68 0.036 TMPRSS2 0.72 0.015 0.67 <.001 TNFRSF10A 0.69 0.010 TNFRSF10B 0.67 0.007 0.64 0.001 TNFRSF18 0.38 0.003 TNFSF10 0.71 0.025 TP53 0.68 0.004 0.57 <.001 TP63 0.75 0.049 0.52 <.001 TPM2 0.62 0.007 TRAF3IP2 0.71 0.017 0.68 0.005 TRO 0.72 0.033 TUBB2A 0.69 0.038 VCL 0.62 <.001 VEGFA 0.71 0.037 WWOX 0.65 0.004 ZFHX3 0.77 0.011 0.73 0.012 ZFP36 0.69 0.018 ZNF827 0.68 0.013 0.49 <.001

Tables 9A and 9B provide genes significantly associated (p<0.05), positively or negatively, with TMPRSS fusion status in the primary Gleason pattern. Increased expression of genes in Table 9A are positively associated with TMPRSS fusion positivity, while increased expression of genes in Table 10A are negatively associated with TMPRSS fusion positivity.

TABLE 9A Genes significantly (p < 0.05) associated with TMPRSS fusion status in the primary Gleason pattern with odds ratio (OR) >1.0 (increased expression is positively associated with TMPRSS fusion positivity Table 9A Official Odds Official Odds Symbol p-value Ratio Symbol p-value Ratio ABCC8 <.001 1.86 MAP3K5 <.001 2.06 ALDH18A1 0.005 1.49 MAP7 <.001 2.74 ALKBH3 0.043 1.30 MSH2 0.005 1.59 ALOX5 <.001 1.66 MSH3 0.006 1.45 AMPD3 <.001 3.92 MUC1 0.012 1.42 APEX1 <.001 2.00 MYO6 <.001 3.79 ARHGDIB <.001 1.87 NCOR2 0.001 1.62 ASAP2 0.019 1.48 NDRG1 <.001 6.77 ATXN1 0.013 1.41 NETO2 <.001 2.63 BMPR1B <.001 2.37 ODC1 <.001 1.98 CACNA1D <.001 9.01 OR51E1 <.001 2.24 CADPS 0.015 1.39 PDE9A <.001 2.21 CD276 0.003 2.25 PEX10 <.001 3.41 CDH1 0.016 1.37 PGK1 0.022 1.33 CDH7 <.001 2.22 PLA2G7 <.001 5.51 CDK7 0.025 1.43 PPP3CA 0.047 1.38 COL9A2 <.001 2.58 PSCA 0.013 1.43 CRISP3 <.001 2.60 PSMD13 0.004 1.51 CTNND1 0.033 1.48 PTCH1 0.022 1.38 ECE1 <.001 2.22 PTK2 0.014 1.38 EIF5 0.023 1.34 PTK6 <.001 2.29 EPHB4 0.005 1.51 PTK7 <.001 2.45 ERG <.001 14.5 PTPRK <.001 1.80 FAM171B 0.047 1.32 RAB30 0.001 1.60 FAM73A 0.008 1.45 REG4 0.018 1.58 FASN 0.004 1.50 RELA 0.001 1.62 GNPTAB <.001 1.60 RFX1 0.020 1.43 GPS1 0.006 1.45 RGS10 <.001 1.71 GRB7 0.023 1.38 SCUBE2 0.009 1.48 HDAC1 <.001 4.95 SEPT9 <.001 3.91 HGD <.001 1.64 SH3RF2 0.004 1.48 HIP1 <.001 1.90 SH3YL1 <.001 1.87 HNF1B <.001 3.55 SHH <.001 2.45 HSPA8 0.041 1.32 SIM2 <.001 1.74 IGF1R 0.001 1.73 SIPA1L1 0.021 1.35 ILF3 <.001 1.91 SLC22A3 <.001 1.63 IMMT 0.025 1.36 SLC44A1 <.001 1.65 ITPR1 <.001 2.72 SPINT1 0.017 1.39 ITPR3 <.001 5.91 TFDP1 0.005 1.75 JAG1 0.007 1.42 TMPRSS2ERGA 0.002 14E5 KCNN2 <.001 2.80 TMPRSS2ERGB <.001 1.97 KHDRBS3 <.001 2.63 TRIM14 <.001 1.65 KIAA0247 0.019 1.38 TSTA3 0.018 1.38 KLK11 <.001 1.98 UAP1 0.046 1.39 LAMC1 0.008 1.56 UBE2G1 0.001 1.66 LAMC2 <.001 3.30 UGDH <.001 2.22 LOX 0.009 1.41 XRCC5 <.001 1.66 LRP1 0.044 1.30 ZMYND8 <.001 2.19

TABLE 9B Genes significantly (p < 0.05) associated with TMPRSS fusion status in the primary Gleason pattern with odds ratio (OR) <1.0 (increased expression is negatively associated with TMPRSS fusion positivity) Table 9B Official Symbol p-value Odds Ratio ABCC4 0.045 0.77 ABHD2 <.001 0.38 ACTR2 0.027 0.73 ADAMTS1 0.024 0.58 ADH5 <.001 0.58 AGTR2 0.016 0.64 AKAP1 0.013 0.70 AKT2 0.015 0.71 ALCAM <.001 0.45 ALDH1A2 0.004 0.70 ANPEP <.001 0.43 ANXA2 0.010 0.71 APC 0.036 0.73 APOC1 0.002 0.56 APOE <.001 0.44 ARF1 0.041 0.77 ATM 0.036 0.74 AURKB <.001 0.62 AZGP1 <.001 0.54 BBC3 0.030 0.74 BCL2 0.012 0.70 BIN1 0.021 0.74 BTG1 0.004 0.67 BTG3 0.003 0.63 C7 0.023 0.74 CADM1 0.007 0.69 CASP1 0.011 0.70 CAV1 0.011 0.71 CCND1 0.019 0.72 CCR1 0.022 0.73 CD44 <.001 0.57 CD68 <.001 0.54 CD82 0.002 0.66 CDH5 0.007 0.66 CDKN1A <.001 0.60 CDKN2B <.001 0.54 CDKN2C 0.012 0.72 CDKN3 0.037 0.77 CHN1 0.038 0.75 CKS2 <.001 0.48 COL11A1 0.017 0.72 COL1A1 <.001 0.59 COL1A2 0.001 0.62 COL3A1 0.027 0.73 COL4A1 0.043 0.76 COL5A1 0.039 0.74 COL5A2 0.026 0.73 COL6A1 0.008 0.66 COL6A3 <.001 0.59 COL8A1 0.022 0.74 CSF1 0.011 0.70 CTNNB1 0.021 0.69 CTSB <.001 0.62 CTSD 0.036 0.68 CTSK 0.007 0.70 CTSS 0.002 0.64 CXCL12 <.001 0.48 CXCR4 0.005 0.68 CXCR7 0.046 0.76 CYR61 0.004 0.65 DAP 0.002 0.64 DARC 0.021 0.73 DDR2 0.021 0.73 DHRS9 <.001 0.52 DIAPH1 <.001 0.56 DICER1 0.029 0.75 DLC1 0.013 0.72 DLGAP1 <.001 0.60 DLL4 <.001 0.57 DPT 0.006 0.68 DUSP1 0.012 0.68 DUSP6 0.001 0.62 DVL1 0.037 0.75 EFNB2 <.001 0.32 EGR1 0.003 0.65 ELK4 <.001 0.60 ERBB2 <.001 0.61 ERBB3 0.045 0.76 ESR2 0.010 0.70 ETV1 0.042 0.74 FABP5 <.001 0.21 FAM13C 0.006 0.67 FCGR3A 0.018 0.72 FGF17 0.009 0.71 FGF6 0.011 0.70 FGF7 0.003 0.63 FN1 0.006 0.69 FOS 0.035 0.74 FOXP3 0.010 0.71 GABRG2 0.029 0.74 GADD45B 0.003 0.63 GDF15 <.001 0.54 GPM6B 0.004 0.67 GPNMB 0.001 0.62 GSN 0.009 0.69 HLA-G 0.050 0.74 HLF 0.018 0.74 HPS1 <.001 0.48 HSD17B3 0.003 0.60 HSD17B4 <.001 0.56 HSPB1 <.001 0.38 HSPB2 0.002 0.62 IFI30 0.049 0.75 IFNG 0.006 0.64 IGF1 0.016 0.73 IGF2 0.001 0.57 IGFBP2 <.001 0.51 IGFBP3 <.001 0.59 IGFBP6 <.001 0.57 IL10 <.001 0.62 IL17A 0.012 0.63 ILIA 0.011 0.59 IL2 0.001 0.63 IL6ST <.001 0.52 INSL4 0.014 0.71 ITGA1 0.009 0.69 ITGA4 0.007 0.68 JUN <.001 0.59 KIT <.001 0.64 KRT76 0.016 0.70 LAG3 0.002 0.63 LAPTM5 <.001 0.58 LGALS3 <.001 0.53 LTBP2 0.011 0.71 LUM 0.012 0.70 MAOA 0.020 0.73 MAP4K4 0.007 0.68 MGST1 <.001 0.54 MMP2 <.001 0.61 MPPED2 <.001 0.45 MRC1 0.005 0.67 MTPN 0.002 0.56 MTSS1 <.001 0.53 MVP 0.009 0.72 MYBPC1 <.001 0.51 MYLK3 0.001 0.58 NCAM1 <.001 0.59 NCAPD3 <.001 0.40 NCOR1 0.004 0.69 NFKBIA <.001 0.63 NNMT 0.006 0.66 NPBWR1 0.027 0.67 OAZ1 0.049 0.64 OLFML3 <.001 0.56 OSM <.001 0.64 PAGE1 0.012 0.52 PDGFRB 0.016 0.73 PECAM1 <.001 0.55 PGR 0.048 0.77 PIK3CA <.001 0.55 PIK3CG 0.008 0.71 PLAU 0.044 0.76 PLK1 0.006 0.68 PLOD2 0.013 0.71 PLP2 0.024 0.73 PNLIPRP2 0.009 0.70 PPAP2B <.001 0.62 PRKAR2B <.001 0.61 PRKCB 0.044 0.76 PROS1 0.005 0.67 PTEN <.001 0.47 PTGER3 0.007 0.69 PTH1R 0.011 0.70 PTK2B <.001 0.61 PTPN1 0.028 0.73 RAB27A <.001 0.21 RAD51 <.001 0.51 RAD9A 0.030 0.75 RARB <.001 0.62 RASSF1 0.038 0.76 RECK 0.009 0.62 RHOB 0.004 0.64 RHOC <.001 0.56 RLN1 <.001 0.30 RND3 0.014 0.72 S100P 0.002 0.66 SDC2 <.001 0.61 SEMA3A 0.001 0.64 SMAD4 <.001 0.64 SPARC <.001 0.59 SPARCL1 <.001 0.56 SPINK1 <.001 0.26 SRD5A1 0.039 0.76 STAT1 0.026 0.74 STS 0.006 0.64 SULF1 <.001 0.53 TFF3 <.001 0.19 TGFA 0.002 0.65 TGFB1I1 0.040 0.77 TGFB2 0.003 0.66 TGFB3 <.001 0.54 TGFBR2 <.001 0.61 THY1 <.001 0.63 TIMP2 0.004 0.66 TIMP3 <.001 0.60 TMPRSS2 <.001 0.40 TNFSF11 0.026 0.63 TPD52 0.002 0.64 TRAM1 <.001 0.45 TRPC6 0.002 0.64 TUBB2A <.001 0.49 VCL <.001 0.57 VEGFB 0.033 0.73 VEGFC <.001 0.61 VIM 0.012 0.69 WISP1 0.030 0.75 WNT5A <.001 0.50

A molecular field effect was investigated, and determined that the expression levels of histologically normal-appearing cells adjacent to the tumor exhibited a molecular signature of prostate cancer. Tables 10A and 10B provide genes significantly associated (p<0.05), positively or negatively, with cRFI or bRFI in non-tumor samples. Table 10A is negatively associated with good prognosis, while increased expression of genes in Table 10B is positively associated with good prognosis.

TABLE 10A Genes significantly (p < 0.05) associated with cRFI or bRFI in Non-Tumor Samples with hazard ratio (HR) >1.0 (increased expression is negatively associated with good prognosis) Table 10A cRFI bRFI Official Symbol HR p-value HR p-value ALCAM 1.278 0.036 ASPN 1.309 0.032 BAG5 1.458 0.004 BRCA2 1.385 <.001 CACNA1D 1.329 0.035 CD164 1.339 0.020 CDKN2B 1.398 0.014 COL3A1 1.300 0.035 COL4A1 1.358 0.019 CTNND2 1.370 0.001 DARC 1.451 0.003 DICER1 1.345 <.001 DPP4 1.358 0.008 EFNB2 1.323 0.007 FASN 1.327 0.035 GHR 1.332 0.048 HSPA5 1.260 0.048 INHBA 1.558 <.001 KCNN2 1.264 0.045 KRT76 1.115 <.001 LAMC1 1.390 0.014 LAMC2 1.216 0.042 LIG3 1.313 0.030 MAOA 1.405 0.013 MCM6 1.307 0.036 MKI67 1.271 0.008 NEK2 1.312 0.016 NPBWR1 1.278 0.035 ODC1 1.320 0.010 PEX10 1.361 0.014 PGK1 1.488 0.004 PLA2G7 1.337 0.025 POSTN 1.306 0.043 PTK6 1.344 0.005 REG4 1.348 0.009 RGS7 1.144 0.047 SFRP4 1.394 0.009 TARP 1.412 0.011 TFF1 1.346 0.010 TGFBR2 1.310 0.035 THY1 1.300 0.038 TMPRSS2ERGA 1.333 <.001 TPD52 1.374 0.015 TRPC6 1.272 0.046 UBE2C 1.323 0.007 UHRF1 1.325 0.021

TABLE 10B Genes significantly (p < 0.05) associated with cRFI or bRFI in Non-Tumor Samples with hazard ratio (HR) <1.0 (increased expression is positively associated with good prognosis) Table 10B cRFI bRFI Official Symbol HR p-value HR p-value ABCA5 0.807 0.028 ABCC3 0.760 0.019 0.750 0.003 ABHD2 0.781 0.028 ADAM15 0.718 0.005 AKAP1 0.740 0.009 AMPD3 0.793 0.013 ANGPT2 0.752 0.027 ANXA2 0.776 0.035 APC 0.755 0.014 APRT 0.762 0.025 AR 0.752 0.015 ARHGDIB 0.753 <.001 BIN1 0.738 0.016 CADM1 0.711 0.004 CCNH 0.820 0.041 CCR1 0.749 0.007 CDK14 0.772 0.014 CDK3 0.819 0.044 CDKN1C 0.808 0.038 CHAF1A 0.634 0.002 0.779 0.045 CHN1 0.803 0.034 CHRAC1 0.751 0.014 0.779 0.021 COL5A1 0.736 0.012 COL5A2 0.762 0.013 COL6A1 0.757 0.032 COL6A3 0.757 0.019 CSK 0.663 <.001 0.698 <.001 CTSK 0.782 0.029 CXCL12 0.771 0.037 CXCR7 0.753 0.008 CYP3A5 0.790 0.035 DDIT4 0.725 0.017 DIAPH1 0.771 0.015 DLC1 0.744 0.004 0.807 0.015 DLGAP1 0.708 0.004 DUSP1 0.740 0.034 EDN1 0.742 0.010 EGR1 0.731 0.028 EIF3H 0.761 0.024 EIF4E 0.786 0.041 ERBB2 0.664 0.001 ERBB4 0.764 0.036 ERCC1 0.804 0.041 ESR2 0.757 0.025 EZH2 0.798 0.048 FAAH 0.798 0.042 FAM13C 0.764 0.012 FAM171B 0.755 0.005 FAM49B 0.811 0.043 FAM73A 0.778 0.015 FASLG 0.757 0.041 FGFR2 0.735 0.016 FOS 0.690 0.008 FYN 0.788 0.035 0.777 0.011 GPNMB 0.762 0.011 GSK3B 0.792 0.038 HGD 0.774 0.017 HIRIP3 0.802 0.033 HSP90AB1 0.753 0.013 HSPB1 0.764 0.021 HSPE1 0.668 0.001 IFI30 0.732 0.002 IGF2 0.747 0.006 IGFBP5 0.691 0.006 IL6ST 0.748 0.010 IL8 0.785 0.028 IMMT 0.708 <.001 ITGA6 0.747 0.008 ITGAV 0.792 0.016 ITGB3 0.814 0.034 ITPR3 0.769 0.009 JUN 0.655 0.005 KHDRBS3 0.764 0.012 KLF6 0.714 <.001 KLK2 0.813 0.048 LAMA4 0.702 0.009 LAMA5 0.744 0.011 LAPTM5 0.740 0.009 LGALS3 0.773 0.036 0.788 0.024 LIMS1 0.807 0.012 MAP3K5 0.815 0.034 MAP3K7 0.809 0.032 MAP4K4 0.735 0.018 0.761 0.010 MAPKAPK3 0.754 0.014 MICA 0.785 0.019 MTA1 0.808 0.043 MVP 0.691 0.001 MYLK3 0.730 0.039 MYO6 0.780 0.037 NCOA1 0.787 0.040 NCOR1 0.876 0.020 NDRG1 0.761 <.001 NFAT5 0.770 0.032 NFKBIA 0.799 0.018 NME2 0.753 0.005 NUP62 0.842 0.032 OAZ1 0.803 0.043 OLFML2B 0.745 0.023 OLFML3 0.743 0.009 OSM 0.726 0.018 PCA3 0.714 0.019 PECAM1 0.774 0.023 PIK3C2A 0.768 0.001 PIM1 0.725 0.011 PLOD2 0.713 0.008 PPP3CA 0.768 0.040 PROM1 0.482 <.001 PTEN 0.807 0.012 PTGS2 0.726 0.011 PTTG1 0.729 0.006 PYCARD 0.783 0.012 RAB30 0.730 0.002 RAGE 0.792 0.012 RFX1 0.789 0.016 0.792 0.010 RGS10 0.781 0.017 RUNX1 0.747 0.007 SDHC 0.827 0.036 SEC23A 0.752 0.010 SEPT9 0.889 0.006 SERPINA3 0.738 0.013 SLC25A21 0.788 0.045 SMARCD1 0.788 0.010 0.733 0.007 SMO 0.813 0.035 SRC 0.758 0.026 SRD5A2 0.738 0.005 ST5 0.767 0.022 STAT5A 0.784 0.039 TGFB2 0.771 0.027 TGFB3 0.752 0.036 THBS2 0.751 0.015 TNFRSF10B 0.739 0.010 TPX2 0.754 0.023 TRAF3IP2 0.774 0.015 TRAM1 0.868 <.001 0.880 <.001 TRIM14 0.785 0.047 TUBB2A 0.705 0.010 TYMP 0.778 0.024 UAP1 0.721 0.013 UTP23 0.763 0.007 0.826 0.018 VCL 0.837 0.040 VEGFA 0.755 0.009 WDR19 0.724 0.005 YBX1 0.786 0.027 ZFP36 0.744 0.032 ZNF827 0.770 0.043

Table 11 provides genes that are significantly associated (p<0.05) with cRFI or bRFI after adjustment for Gleason pattern or highest Gleason pattern.

TABLE 11 Genes significantly (p < 0.05) associated with cRFI or bRFI after adjustment for Gleason pattern in the primary Gleason pattern or highest Gleason pattern Some HR <=1.0 and some HR > 1.0 cRFI bRFI bRFI Highest Primary Highest Table 11 Pattern Pattern Pattern Official Symbol HR p-value HR p-value HR p-value HSPA5 0.710 0.009 1.288 0.030 ODC1 0.741 0.026 1.343 0.004 1.261 0.046

Tables 12A and 12B provide genes that are significantly associated (p<0.05) with prostate cancer specific survival (PCSS) in the primary Gleason pattern. Increased expression of genes in Table 12A is negatively associated with good prognosis, while increased expression of genes in Table 12B is positively associated with good prognosis.

TABLE 12A Genes significantly (p < 0.05) associated with prostate cancer specific survival (PCSS) in the Primary Gleason Pattern HR >1.0 (Increased expression is negatively associated with good prognosis) Table 12A Official Official Symbol HR p-value Symbol HR p-value AKR1C3 1.476 0.016 GREM1 1.942 <.001 ANLN 1.517 0.006 IFI30 1.482 0.048 APOC1 1.285 0.016 IGFBP3 1.513 0.027 APOE 1.490 0.024 INHBA 3.060 <.001 ASPN 3.055 <.001 KIF4A 1.355 0.001 ATP5E 1.788 0.012 KLK14 1.187 0.004 AURKB 1.439 0.008 LAPTM5 1.613 0.006 BGN 2.640 <.001 LTBP2 2.018 <.001 BIRC5 1.611 <.001 MMP11 1.869 <.001 BMP6 1.490 0.021 MYBL2 1.737 0.013 BRCA1 1.418 0.036 NEK2 1.445 0.028 CCNB1 1.497 0.021 NOX4 2.049 <.001 CD276 1.668 0.005 OLFML2B 1.497 0.023 CDC20 1.730 <.001 PLK1 1.603 0.006 CDH11 1.565 0.017 POSTN 2.585 <.001 CDH7 1.553 0.007 PPFIA3 1.502 0.012 CDKN2B 1.751 0.003 PTK6 1.527 0.009 CDKN2C 1.993 0.013 PTTG1 1.382 0.029 CDKN3 1.404 0.008 RAD51 1.304 0.031 CENPF 2.031 <.001 RGS7 1.251 <.001 CHAF1A 1.376 0.011 RRM2 1.515 <.001 CKS2 1.499 0.031 SAT1 1.607 0.004 COL1A1 2.574 <.001 SDC1 1.710 0.007 COL1A2 1.607 0.011 SESN3 1.399 0.045 COL3A1 2.382 <.001 SFRP4 2.384 <.001 COL4A1 1.970 <.001 SHMT2 1.949 0.003 COL5A2 1.938 0.002 SPARC 2.249 <.001 COL8A1 2.245 <.001 STMN1 1.748 0.021 CTHRC1 2.085 <.001 SULF1 1.803 0.004 CXCR4 1.783 0.007 THBS2 2.576 <.001 DDIT4 1.535 0.030 THY1 1.908 0.001 DYNLL1 1.719 0.001 TK1 1.394 0.004 F2R 2.169 <.001 TOP2A 2.119 <.001 FAM171B 1.430 0.044 TPX2 2.074 0.042 FAP 1.993 0.002 UBE2C 1.598 <.001 FCGR3A 2.099 <.001 UGT2B15 1.363 0.016 FN1 1.537 0.024 UHRF1 1.642 0.001 GPR68 1.520 0.018 ZWINT 1.570 0.010

TABLE 12B Genes significantly (p < 0.05) associated with prostate cancer specific survival (PCSS) in the Primary Gleason Pattern HR <1.0 (Increased expression is positively associated with good prognosis) Table 12B Official Official Symbol HR p-value Symbol HR p-value AAMP 0.649 0.040 IGFBP6 0.578 0.003 ABCA5 0.777 0.015 IL2 0.528 0.010 ABCG2 0.715 0.037 IL6ST 0.574 <.001 ACOX2 0.673 0.016 IL8 0.540 0.001 ADH5 0.522 <.001 ING5 0.688 0.015 ALDH1A2 0.561 <.001 ITGA6 0.710 0.005 AMACR 0.693 0.029 ITGA7 0.676 0.033 AMPD3 0.750 0.049 JUN 0.506 0.001 ANPEP 0.531 <.001 KIT 0.628 0.047 ATXN1 0.640 0.011 KLK1 0.523 0.002 AXIN2 0.657 0.002 KLK2 0.581 <.001 AZGP1 0.617 <.001 KLK3 0.676 <.001 BDKRB1 0.553 0.032 KRT15 0.684 0.005 BIN1 0.658 <.001 KRT18 0.536 <.001 BTRC 0.716 0.011 KRT5 0.673 0.004 C7 0.531 <.001 KRT8 0.613 0.006 CADM1 0.646 0.015 LAMB3 0.740 0.027 CASP7 0.538 0.029 LGALS3 0.678 0.007 CCNH 0.674 0.001 MGST1 0.640 0.002 CD164 0.606 <.001 MPPED2 0.629 <.001 CD44 0.687 0.016 MTSS1 0.705 0.041 CDK3 0.733 0.039 MYBPC1 0.534 <.001 CHN1 0.653 0.014 NCAPD3 0.519 <.001 COL6A1 0.681 0.015 NFAT5 0.536 <.001 CSF1 0.675 0.019 NRG1 0.467 0.007 CSRP1 0.711 0.007 OLFML3 0.646 0.001 CXCL12 0.650 0.015 OMD 0.630 0.006 CYP3A5 0.507 <.001 OR51E2 0.762 0.017 CYR61 0.569 0.007 PAGE4 0.518 <.001 DLGAP1 0.654 0.004 PCA3 0.581 <.001 DNM3 0.692 0.010 PGF 0.705 0.038 DPP4 0.544 <.001 PPAP2B 0.568 <.001 DPT 0.543 <.001 PPP1R12A 0.694 0.017 DUSP1 0.660 0.050 PRIMA1 0.678 0.014 DUSP6 0.699 0.033 PRKCA 0.632 0.001 EGR1 0.490 <.001 PRKCB 0.692 0.028 EGR3 0.561 <.001 PROM1 0.393 0.017 EIF5 0.720 0.035 PTEN 0.689 0.002 ERBB3 0.739 0.042 PTGS2 0.611 0.004 FAAH 0.636 0.010 PTH1R 0.629 0.031 FAM107A 0.541 <.001 RAB27A 0.721 0.046 FAM13C 0.526 <.001 RND3 0.678 0.029 FAS 0.689 0.030 RNF114 0.714 0.035 FGF10 0.657 0.024 SDHC 0.590 <.001 FKBP5 0.699 0.040 SERPINA3 0.710 0.050 FLNC 0.742 0.036 SH3RF2 0.570 0.005 FOS 0.556 0.005 SLC22A3 0.517 <.001 FOXQ1 0.666 0.007 SMAD4 0.528 <.001 GADD45B 0.554 0.002 SMO 0.751 0.026 GDF15 0.659 0.009 SRC 0.667 0.004 GHR 0.683 0.027 SRD5A2 0.488 <.001 GPM6B 0.666 0.005 STAT5B 0.700 0.040 GSN 0.646 0.006 SVIL 0.694 0.024 GSTM1 0.672 0.006 TFF3 0.701 0.045 GSTM2 0.514 <.001 TGFB1I1 0.670 0.029 HGD 0.771 0.039 TGFB2 0.646 0.010 HIRIP3 0.730 0.013 TNFRSF10B 0.685 0.014 HK1 0.778 0.048 TNFSF10 0.532 <.001 HLF 0.581 <.001 TPM2 0.623 0.005 HNF1B 0.643 0.013 TRO 0.767 0.049 HSD17B10 0.742 0.029 TUBB2A 0.613 0.003 IER3 0.717 0.049 VEGFB 0.780 0.034 IGF1 0.612 <.001 ZFP36 0.576 0.001 ZNF827 0.644 0.014

Analysis of gene expression and upgrading/upstaging was based on univariate ordinal logistic regression models using weighted maximum likelihood estimators for each gene in the gene list (727 test genes and 5 reference genes). P-values were generated using a Wald test of the null hypothesis that the odds ratio (OR) is one. Both unadjusted p-values and the q-value (smallest FDR at which the hypothesis test in question is rejected) were reported. Un-adjusted p-values <0.05 were considered statistically significant. Since two tumor specimens were selected for each patient, this analysis was performed using the 2 specimens from each patient as follows: (1) analysis using the primary Gleason pattern specimen from each patient (Specimens A1 and B2 as described in Table 2); and (2) analysis using the highest Gleason pattern specimen from each patient (Specimens A1 and B1 as described in Table 2). 200 genes were found to be significantly associated (p<0.05) with upgrading/upstaging in the primary Gleason pattern sample (PGP) and 203 genes were found to be significantly associated (p<0.05) with upgrading/upstaging in the highest Gleason pattern sample (HGP).

Tables 13A and 13B provide genes significantly associated (p<0.05), positively or negatively, with upgrading/upstaging in the primary and/or highest Gleason pattern. Increased expression of genes in Table 13A is positively associated with higher risk of upgrading/upstaging (poor prognosis), while increased expression of genes in Table 13B is negatively associated with risk of upgrading/upstaging (good prognosis).

TABLE 13A Genes significantly (p < 0.05) associated with upgrading/ upstaging in the Primary Gleason Pattern (PGP) and Highest Gleason Pattern (HGP) OR >1.0 (Increased expression is positively associated with higher risk of upgrading/upstaging (poor prognosis)) Table 13A PGP HGP Gene OR p-value OR p-value ALCAM 1.52 0.0179 1.50 0.0184 ANLN 1.36 0.0451 . . APOE 1.42 0.0278 1.50 0.0140 ASPN 1.60 0.0027 2.06 0.0001 AURKA 1.47 0.0108 . . AURKB . . 1.52 0.0070 BAX . . 1.48 0.0095 BGN 1.58 0.0095 1.73 0.0034 BIRC5 1.38 0.0415 . . BMP6 1.51 0.0091 1.59 0.0071 BUB1 1.38 0.0471 1.59 0.0068 CACNA1D 1.36 0.0474 1.52 0.0078 CASP7 . . 1.32 0.0450 CCNE2 1.54 0.0042 . . CD276 . . 1.44 0.0265 CDC20 1.35 0.0445 1.39 0.0225 CDKN2B . . 1.36 0.0415 CENPF 1.43 0.0172 1.48 0.0102 CLTC 1.59 0.0031 1.57 0.0038 COL1A1 1.58 0.0045 1.75 0.0008 COL3A1 1.45 0.0143 1.47 0.0131 COL8A1 1.40 0.0292 1.43 0.0258 CRISP3 . . 1.40 0.0256 CTHRC1 . . 1.56 0.0092 DBN1 1.43 0.0323 1.45 0.0163 DIAPH1 1.51 0.0088 1.58 0.0025 DICER1 . . 1.40 0.0293 DIO2 . . 1.49 0.0097 DVL1 . . 1.53 0.0160 F2R 1.46 0.0346 1.63 0.0024 FAP 1.47 0.0136 1.74 0.0005 FCGR3A . . 1.42 0.0221 HPN . . 1.36 0.0468 HSD17B4 . . 1.47 0.0151 HSPA8 1.65 0.0060 1.58 0.0074 IL11 1.50 0.0100 1.48 0.0113 IL1B 1.41 0.0359 . . INHBA 1.56 0.0064 1.71 0.0042 KHDRBS3 1.43 0.0219 1.59 0.0045 KIF4A . . 1.50 0.0209 KPNA2 1.40 0.0366 . . KRT2 . . 1.37 0.0456 KRT75 . . 1.44 0.0389 MANF . . 1.39 0.0429 MELK 1.74 0.0016 . . MKI67 1.35 0.0408 . . MMP11 . . 1.56 0.0057 NOX4 1.49 0.0105 1.49 0.0138 PLAUR 1.44 0.0185 . . PLK1 . . 1.41 0.0246 PTK6 . . 1.36 0.0391 RAD51 . . 1.39 0.0300 RAF1 . . 1.58 0.0036 RRM2 1.57 0.0080 . . SESN3 1.33 0.0465 . . SFRP4 2.33 <0.0001 2.51 0.0015 SKIL 1.44 0.0288 1.40 0.0368 SOX4 1.50 0.0087 1.59 0.0022 SPINK1 1.52 0.0058 . . SPP1 . . 1.42 0.0224 THBS2 . . 1.36 0.0461 TK1 . . 1.38 0.0283 TOP2A 1.85 0.0001 1.66 0.0011 TPD52 1.78 0.0003 1.64 0.0041 TPX2 1.70 0.0010 . . UBE2G1 1.38 0.0491 . . UBE2T 1.37 0.0425 1.46 0.0162 UHRF1 . . 1.43 0.0164 VCPIP1 . . 1.37 0.0458

TABLE 13B Genes significantly (p < 0.05) associated with upgrading/ upstaging in the Primary Gleason Pattern (PGP) and Highest Gleason Pattern (HGP) OR <1.0 (Increased expression is negatively associated with higher risk of upgrading/upstaging (good prognosis)) Table 13B PGP HGP Gene OR p-value OR p-value ABCC3 . . 0.70 0.0216 ABCC8 0.66 0.0121 . . ABCG2 0.67 0.0208 0.61 0.0071 ACE . . 0.73 0.0442 ACOX2 0.46 0.0000 0.49 0.0001 ADH5 0.69 0.0284 0.59 0.0047 AIG1 . . 0.60 0.0045 AKR1C1 . . 0.66 0.0095 ALDH1A2 0.36 <0.0001 0.36 <0.0001 ALKBH3 0.70 0.0281 0.61 0.0056 ANPEP . . 0.68 0.0109 ANXA2 0.73 0.0411 0.66 0.0080 APC . . 0.68 0.0223 ATXN1 . . 0.70 0.0188 AXIN2 0.60 0.0072 0.68 0.0204 AZGP1 0.66 0.0089 0.57 0.0028 BCL2 . . 0.71 0.0182 BIN1 0.55 0.0005 . . BTRC 0.69 0.0397 0.70 0.0251 C7 0.53 0.0002 0.51 <0.0001 CADM1 0.57 0.0012 0.60 0.0032 CASP1 0.64 0.0035 0.72 0.0210 CAV1 0.64 0.0097 0.59 0.0032 CAV2 . . 0.58 0.0107 CD164 . . 0.69 0.0260 CD82 0.67 0.0157 0.69 0.0167 CDH1 0.61 0.0012 0.70 0.0210 CDK14 0.70 0.0354 . . CDK3 . . 0.72 0.0267 CDKN1C 0.61 0.0036 0.56 0.0003 CHN1 0.71 0.0214 . . COL6A1 0.62 0.0125 0.60 0.0050 COL6A3 0.65 0.0080 0.68 0.0181 CSRP1 0.43 0.0001 0.40 0.0002 CTSB 0.66 0.0042 0.67 0.0051 CTSD 0.64 0.0355 . . CTSK 0.69 0.0171 . . CTSL1 0.72 0.0402 . . CUL1 0.61 0.0024 0.70 0.0120 CXCL12 0.69 0.0287 0.63 0.0053 CYP3A5 0.68 0.0099 0.62 0.0026 DDR2 0.68 0.0324 0.62 0.0050 DES 0.54 0.0013 0.46 0.0002 DHX9 0.67 0.0164 . . DLGAP1 . . 0.66 0.0086 DPP4 0.69 0.0438 0.69 0.0132 DPT 0.59 0.0034 0.51 0.0005 DUSP1 . . 0.67 0.0214 EDN1 . . 0.66 0.0073 EDNRA 0.66 0.0148 0.54 0.0005 EIF2C2 . . 0.65 0.0087 ELK4 0.55 0.0003 0.58 0.0013 ENPP2 0.65 0.0128 0.59 0.0007 EPHA3 0.71 0.0397 0.73 0.0455 EPHB2 0.60 0.0014 . . EPHB4 0.73 0.0418 . . EPHX3 . . 0.71 0.0419 ERCC1 0.71 0.0325 . . FAM107A 0.56 0.0008 0.55 0.0011 FAM13C 0.68 0.0276 0.55 0.0001 FAS 0.72 0.0404 . . FBN1 0.72 0.0395 . . FBXW7 0.69 0.0417 . . FGF10 0.59 0.0024 0.51 0.0001 FGF7 0.51 0.0002 0.56 0.0007 FGFR2 0.54 0.0004 0.47 <0.0001 FLNA 0.58 0.0036 0.50 0.0002 FLNC 0.45 0.0001 0.40 <0.0001 FLT4 0.61 0.0045 . . FOXO1 0.55 0.0005 0.53 0.0005 FOXP3 0.71 0.0275 0.72 0.0354 GHR 0.59 0.0074 0.53 0.0001 GNRH1 0.72 0.0386 . . GPM6B 0.59 0.0024 0.52 0.0002 GSN 0.65 0.0107 0.65 0.0098 GSTM1 0.44 <0.0001 0.43 <0.0001 GSTM2 0.42 <0.0001 0.39 <0.0001 HLF 0.46 <0.0001 0.47 0.0001 HPS1 0.64 0.0069 0.69 0.0134 HSPA5 0.68 0.0113 . . HSPB2 0.61 0.0061 0.55 0.0004 HSPG2 0.70 0.0359 . . ID3 . . 0.70 0.0245 IGF1 0.45 <0.0001 0.50 0.0005 IGF2 0.67 0.0200 0.68 0.0152 IGFBP2 0.59 0.0017 0.69 0.0250 IGFBP6 0.49 <0.0001 0.64 0.0092 IL6ST 0.56 0.0009 0.60 0.0012 ILK 0.51 0.0010 0.49 0.0004 ITGA1 0.58 0.0020 0.58 0.0016 ITGA3 0.71 0.0286 0.70 0.0221 ITGA5 . . 0.69 0.0183 ITGA7 0.56 0.0035 0.42 <0.0001 ITGB1 0.63 0.0095 0.68 0.0267 ITGB3 0.62 0.0043 0.62 0.0040 ITPR1 0.62 0.0032 . . JUN 0.73 0.0490 0.68 0.0152 KIT 0.55 0.0003 0.57 0.0005 KLC1 . . 0.70 0.0248 KLK1 . . 0.60 0.0059 KRT15 0.58 0.0009 0.45 <0.0001 KRT5 0.70 0.0262 0.59 0.0008 LAMA4 0.56 0.0359 0.68 0.0498 LAMB3 . . 0.60 0.0017 LGALS3 0.58 0.0007 0.56 0.0012 LRP1 0.69 0.0176 . . MAP3K7 0.70 0.0233 0.73 0.0392 MCM3 0.72 0.0320 . . MMP2 0.66 0.0045 0.60 0.0009 MMP7 0.61 0.0015 0.65 0.0032 MMP9 0.64 0.0057 0.72 0.0399 MPPED2 0.72 0.0392 0.63 0.0042 MTA1 . . 0.68 0.0095 MTSS1 0.58 0.0007 0.71 0.0442 MVP 0.57 0.0003 0.70 0.0152 MYBPC1 . . 0.70 0.0359 NCAM1 0.63 0.0104 0.64 0.0080 NCAPD3 0.67 0.0145 0.64 0.0128 NEXN 0.54 0.0004 0.55 0.0003 NFAT5 0.72 0.0320 0.70 0.0177 NUDT6 0.66 0.0102 . . OLFML3 0.56 0.0035 0.51 0.0011 OMD 0.61 0.0011 0.73 0.0357 PAGE4 0.42 <0.0001 0.36 <0.0001 PAK6 0.72 0.0335 . . PCDHGB7 0.70 0.0262 0.55 0.0004 PGF 0.72 0.0358 0.71 0.0270 PLP2 0.66 0.0088 0.63 0.0041 PPAP2B 0.44 <0.0001 0.50 0.0001 PPP1R12A 0.45 0.0001 0.40 <0.0001 PRIMA1 . . 0.63 0.0102 PRKAR2B 0.71 0.0226 . . PRKCA 0.34 <0.0001 0.42 <0.0001 PRKCB 0.66 0.0120 0.49 <0.0001 PROM1 0.61 0.0030 . . PTEN 0.59 0.0008 0.55 0.0001 PTGER3 0.67 0.0293 . . PTH1R 0.69 0.0259 0.71 0.0327 PTK2 0.75 0.0461 . . PTK2B 0.70 0.0244 0.74 0.0388 PYCARD 0.73 0.0339 0.67 0.0100 RAD9A 0.64 0.0124 . . RARB 0.67 0.0088 0.65 0.0116 RGS10 0.70 0.0219 . . RHOB . . 0.72 0.0475 RND3 . . 0.67 0.0231 SDHC 0.72 0.0443 . . SEC23A 0.66 0.0101 0.53 0.0003 SEMA3A 0.51 0.0001 0.69 0.0222 SH3RF2 0.55 0.0002 0.54 0.0002 SLC22A3 0.48 0.0001 0.50 0.0058 SMAD4 0.49 0.0001 0.50 0.0003 SMARCC2 0.59 0.0028 0.65 0.0052 SMO 0.60 0.0048 0.52 <0.0001 SORBS1 0.56 0.0024 0.48 0.0002 SPARCL1 0.43 0.0001 0.50 0.0001 SRD5A2 0.26 <0.0001 0.31 <0.0001 ST5 0.63 0.0103 0.52 0.0006 STAT5A 0.60 0.0015 0.61 0.0037 STAT5B 0.54 0.0005 0.57 0.0008 SUMO1 0.65 0.0066 0.66 0.0320 SVIL 0.52 0.0067 0.46 0.0003 TGFB1I1 0.44 0.0001 0.43 0.0000 TGFB2 0.55 0.0007 0.58 0.0016 TGFB3 0.57 0.0010 0.53 0.0005 TIMP1 0.72 0.0224 . . TIMP2 0.68 0.0198 0.69 0.0206 TIMP3 0.67 0.0105 0.64 0.0065 TMPRSS2 . . 0.72 0.0366 TNFRSF10A 0.71 0.0181 . . TNFSF10 0.71 0.0284 . . TOP2B 0.73 0.0432 . . TP63 0.62 0.0014 0.50 <0.0001 TPM1 0.54 0.0007 0.52 0.0002 TPM2 0.41 <0.0001 0.40 <0.0001 TPP2 0.65 0.0122 . . TRA2A 0.72 0.0318 . . TRAF3IP2 0.62 0.0064 0.59 0.0053 TRO 0.57 0.0003 0.51 0.0001 VCL 0.52 0.0005 0.52 0.0004 VIM 0.65 0.0072 0.65 0.0045 WDR19 0.66 0.0097 . . WFDC1 0.58 0.0023 0.60 0.0026 ZFHX3 0.69 0.0144 0.62 0.0046 ZNF827 0.62 0.0030 0.53 0.0001

Example 3 Identification of Micrornas Associated with Clinical Recurrence and Death Due to Prostate Cancer

MicroRNAs function by binding to portions of messenger RNA (mRNA) and changing how frequently the mRNA is translated into protein. They can also influence the turnover of mRNA and thus how long the mRNA remains intact in the cell. Since microRNAs function primarily as an adjunct to mRNA, this study evaluated the joint prognostic value of microRNA expression and gene (mRNA) expression. Since the expression of certain microRNAs may be a surrogate for expression of genes that are not in the assessed panel, we also evaluated the prognostic value of microRNA expression by itself.

Patients and Samples

Samples from the 127 patients with clinical recurrence and 374 patients without clinical recurrence after radical prostatectomy described in Example 2 were used in this study. The final analysis set comprised 416 samples from patients in which both gene expression and microRNA expression were successfully assayed. Of these, 106 patients exhibited clinical recurrence and 310 did not have clinical recurrence. Tissue samples were taken from each prostate sample representing (1) the primary Gleason pattern in the sample, and (2) the highest Gleason pattern in the sample. In addition, a sample of histologically normal-appearing tissue adjacent to the tumor (NAT) was taken. The number of patients in the analysis set for each tissue type and the number of them who experienced clinical recurrence or death due to prostate cancer are shown in Table 14.

TABLE 14 Number of Patients and Events in Analysis Set Clinical Deaths Due to Patients Recurrences Prostate Cancer Primary Gleason Pattern Tumor Tissue 416 106 36 Highest Gleason Pattern Tumor Tissue 405 102 36 Normal Adjacent Tissue 364 81 29

Assay Method

Expression of 76 test microRNAs and 5 reference microRNAs were determined from RNA extracted from fixed paraffin-embedded (FPE) tissue. MicroRNA expression in all three tissue type was quantified by reverse transcriptase polymerase chain reaction (RT-PCR) using the crossing point (C_(p)) obtained from the Taqman® MicroRNA Assay kit (Applied Biosystems, Inc., Carlsbad, Calif.).

Statistical Analysis

Using univariate proportional hazards regression (Cox D R, Journal of the Royal Statistical Society, Series B 34:187-220, 1972), applying the sampling weights from the cohort sampling design, and using variance estimation based on the Lin and Wei method (Lin and Wei, Journal of the American Statistical Association 84:1074-1078, 1989), microRNA expression, normalized by the average expression for the 5 reference microRNAs hsa-miR-106a, hsa-miR-146b-5p, hsa-miR-191, hsa-miR-19b, and hsa-miR-92a, and reference-normalized gene expression of the 733 genes (including the reference genes) discussed above, were assessed for association with clinical recurrence and death due to prostate cancer. Standardized hazard ratios (the proportional change in the hazard associated with a change of one standard deviation in the covariate value) were calculated.

This analysis included the following classes of predictors:

1. MicroRNAs alone

2. MicroRNA-gene pairs Tier 1

3. MicroRNA-gene pairs Tier 2

4. MicroRNA-gene pairs Tier 3

5. All other microRNA-gene pairs Tier 4

The four tiers were pre-determined based on the likelihood (Tier 1 representing the highest likelihood) that the gene-microRNA pair functionally interacted or that the microRNA was related to prostate cancer based on a review of the literature and existing microarray data sets.

False discovery rates (FDR) (Benjamini and Hochberg, Journal of the Royal Statistical Society, Series B 57:289-300, 1995) were assessed using Efron's separate class methodology (Efron, Annals of Applied Statistics 2:197-223., 2008). The false discovery rate is the expected proportion of the rejected null hypotheses that are rejected incorrectly (and thus are false discoveries). Efron's methodology allows separate FDR assessment (q-values) (Storey, Journal of the Royal Statistical Society, Series B 64:479-498, 2002) within each class while utilizing the data from all the classes to improve the accuracy of the calculation. In this analysis, the q-value for a microRNA or microRNA-gene pair can be interpreted as the empirical Bayes probability that the microRNA or microRNA-gene pair identified as being associated with clinical outcome is in fact a false discovery given the data. The separate class approach was applied to a true discovery rate degree of association (TDRDA) analysis (Crager, Statistics in Medicine 29:33-45, 2010) to determine sets of microRNAs or microRNA-gene pairs that have standardized hazard ratio for clinical recurrence or prostate cancer-specific death of at least a specified amount while controlling the FDR at 10%. For each microRNA or microRNA-gene pair, a maximum lower bound (MLB) standardized hazard ratio was computed, showing the highest lower bound for which the microRNA or microRNA-gene pair was included in a TDRDA set with 10% FDR. Also calculated was an estimate of the true standardized hazard ratio corrected for regression to the mean (RM) that occurs in subsequent studies when the best predictors are selected from a long list (Crager, 2010 above). The RM-corrected estimate of the standardized hazard ratio is a reasonable estimate of what could be expected if the selected microRNA or microRNA-gene pair were studied in a separate, subsequent study.

These analyses were repeated adjusting for clinical and pathology covariates available at the time of patient biopsy: biopsy Gleason score, baseline PSA level, and clinical T-stage (T1-T2A vs. T2B or T2C) to assess whether the microRNAs or microRNA-gene pairs have predictive value independent of these clinical and pathology covariates.

Results

The analysis identified 21 microRNAs assayed from primary Gleason pattern tumor tissue that were associated with clinical recurrence of prostate cancer after radical prostatectomy, allowing a false discovery rate of 10% (Table 15). Results were similar for microRNAs assessed from highest Gleason pattern tumor tissue (Table 16), suggesting that the association of microRNA expression with clinical recurrence does not change markedly depending on the location within a tumor tissue sample. No microRNA assayed from normal adjacent tissue was associated with the risk of clinical recurrence at a false discovery rate of 10%. The sequences of the microRNAs listed in Tables 15-21 are shown in Table B.

TABLE 15 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio 95% Max. Lower RM- q-value^(a) Direction Uncorrected Confidence Bound Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.79 (1.38, 2.32) 1.19 1.51 hsa-miR-106b <0.0001 0.1% (+) 1.80 (1.38, 2.34) 1.19 1.51 hsa-miR-30e-5p <0.0001 0.1% (−) 1.63 (1.30, 2.04) 1.18 1.46 hsa-miR-21 <0.0001 0.1% (+) 1.66 (1.31, 2.09) 1.18 1.46 hsa-miR-133a <0.0001 0.1% (−) 1.72 (1.33, 2.21) 1.18 1.48 hsa-miR-449a <0.0001 0.1% (+) 1.56 (1.26, 1.92) 1.17 1.42 hsa-miR-30a 0.0001 0.1% (−) 1.56 (1.25, 1.94) 1.16 1.41 hsa-miR-182 0.0001 0.2% (+) 1.74 (1.31, 2.31) 1.17 1.45 hsa-miR-27a 0.0002 0.2% (+) 1.65 (1.27, 2.14) 1.16 1.43 hsa-miR-222 0.0006 0.5% (−) 1.47 (1.18, 1.84) 1.12 1.35 hsa-miR-103 0.0036 2.1% (+) 1.77 (1.21, 2.61) 1.12 1.36 hsa-miR-1 0.0037 2.2% (−) 1.32 (1.10, 1.60) 1.07 1.26 hsa-miR-145 0.0053 2.9% (−) 1.34 (1.09, 1.65) 1.07 1.27 hsa-miR-141 0.0060 3.2% (+) 1.43 (1.11, 1.84) 1.07 1.29 hsa-miR-92a 0.0104 4.8% (+) 1.32 (1.07, 1.64) 1.05 1.25 hsa-miR-22 0.0204 7.7% (+) 1.31 (1.03, 1.64) 1.03 1.23 hsa-miR-29b 0.0212 7.9% (+) 1.36 (1.03, 1.76) 1.03 1.24 hsa-miR-210 0.0223 8.2% (+) 1.33 (1.03, 1.70) 1.00 1.23 hsa-miR-486-5p 0.0267 9.4% (−) 1.25 (1.00, 1.53) 1.00 1.20 hsa-miR-19b 0.0280 9.7% (−) 1.24 (1.00, 1.50) 1.00 1.19 hsa-miR-205 0.0289 10.0% (−) 1.25 (1.00, 1.53) 1.00 1.20 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 16 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio 95% Max. Lower RM- q-value^(a) Direction Uncorrected Confidence Bound Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.91 (1.48, 2.47) 1.24 1.59 hsa-miR-449a <0.0001 0.0% (+) 1.75 (1.40, 2.18) 1.23 1.54 hsa-miR-205 <0.0001 0.0% (−) 1.53 (1.29, 1.81) 1.20 1.43 hsa-miR-19b <0.0001 0.0% (−) 1.37 (1.19, 1.57) 1.15 1.32 hsa-miR-106b <0.0001 0.0% (+) 1.84 (1.39, 2.42) 1.22 1.51 hsa-miR-21 <0.0001 0.0% (+) 1.68 (1.32, 2.15) 1.19 1.46 hsa-miR-30a 0.0005 0.4% (−) 1.44 (1.17, 1.76) 1.13 1.33 hsa-miR-30e-5p 0.0010 0.6% (−) 1.37 (1.14, 1.66) 1.11 1.30 hsa-miR-133a 0.0015 0.8% (−) 1.57 (1.19, 2.07) 1.13 1.36 hsa-miR-1 0.0016 0.8% (−) 1.42 (1.14, 1.77) 1.11 1.31 hsa-miR-103 0.0021 1.1% (+) 1.69 (1.21, 2.37) 1.13 1.37 hsa-miR-210 0.0024 1.2% (+) 1.43 (1.13, 1.79) 1.11 1.31 hsa-miR-182 0.0040 1.7% (+) 1.48 (1.13, 1.93) 1.11 1.31 hsa-miR-27a 0.0055 2.1% (+) 1.46 (1.12, 1.91) 1.09 1.30 hsa-miR-222 0.0093 3.2% (−) 1.38 (1.08, 1.77) 1.08 1.27 hsa-miR-331 0.0126 3.9% (+) 1.38 (1.07, 1.77) 1.07 1.26 hsa-miR-191* 0.0143 4.3% (+) 1.38 (1.06, 1.78) 1.07 1.26 hsa-miR-425 0.0151 4.5% (+) 1.40 (1.06, 1.83) 1.07 1.26 hsa-miR-31 0.0176 5.1% (−) 1.29 (1.04, 1.60) 1.05 1.22 hsa-miR-92a 0.0202 5.6% (+) 1.31 (1.03, 1.65) 1.05 1.23 hsa-miR-155 0.0302 7.6% (−) 1.32 (1.00, 1.69) 1.03 1.22 hsa-miR-22 0.0437 9.9% (+) 1.30 (1.00, 1.67) 1.00 1.21 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with death due to prostate cancer is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

Table 17 shows microRNAs assayed from primary Gleason pattern tissue that were identified as being associated with the risk of prostate-cancer-specific death, with a false discovery rate of 10%. Table 18 shows the corresponding analysis for microRNAs assayed from highest Gleason pattern tissue. No microRNA assayed from normal adjacent tissue was associated with the risk of prostate-cancer-specific death at a false discovery rate of 10%.

TABLE 17 MicroRNAs Associated with Death Due to Prostate Cancer Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower 95% Bound RM- q-value^(a) Direction Uncorrected Confidence @10% Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p 0.0001 0.6% (−) 1.88 (1.37, 2.58) 1.15 1.46 hsa-miR-30a 0.0001 0.7% (−) 1.78 (1.33, 2.40) 1.14 1.44 hsa-miR-133a 0.0005 1.2% (−) 1.85 (1.31, 2.62) 1.13 1.41 hsa-miR-222 0.0006 1.4% (−) 1.65 (1.24, 2.20) 1.12 1.38 hsa-miR-106b 0.0024 2.7% (+) 1.85 (1.24, 2.75) 1.11 1.35 hsa-miR-1 0.0028 3.0% (−) 1.43 (1.13, 1.81) 1.08 1.30 hsa-miR-21 0.0034 3.3% (+) 1.63 (1.17, 2.25) 1.09 1.33 hsa-miR-93 0.0044 3.9% (+) 1.87 (1.21, 2.87) 1.09 1.32 hsa-miR-26a 0.0072 5.3% (−) 1.47 (1.11, 1.94) 1.07 1.29 hsa-miR-152 0.0090 6.0% (−) 1.46 (1.10, 1.95) 1.06 1.28 hsa-miR-331 0.0105 6.5% (+) 1.46 (1.09, 1.96) 1.05 1.27 hsa-miR-150 0.0159 8.3% (+) 1.51 (1.07, 2.10) 1.03 1.27 hsa-miR-27b 0.0160 8.3% (+) 1.97 (1.12, 3.42) 1.05 1.25 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with death due to prostate cancer endpoint is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of death due to prostate cancer. ^(c)RM: regression to the mean.

TABLE 18 MicroRNAs Associated with Death Due to Prostate Cancer Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower Bound q-value^(a) Direction Uncorrected 95% Confidence @10% RM-Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval FDR Estimate^(c) hsa-miR-27b 0.0016 6.1% (+) 2.66 (1.45, 4.88) 1.07 1.32 hsa-miR-21 0.0020 6.4% (+) 1.66 (1.21, 2.30) 1.05 1.34 hsa-miR-10a 0.0024 6.7% (+) 1.78 (1.23, 2.59) 1.05 1.34 hsa-miR-93 0.0024 6.7% (+) 1.83 (1.24, 2.71) 1.05 1.34 hsa-miR-106b 0.0028 6.8% (+) 1.79 (1.22, 2.63) 1.05 1.33 hsa-miR-150 0.0035 7.1% (+) 1.61 (1.17, 2.22) 1.05 1.32 hsa-miR-1 0.0104 9.0% (−) 1.52 (1.10, 2.09) 1.00 1.28 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical endpoint is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of death due to prostate cancer. ^(c)RM: regression to the mean.

Table 19 and Table 20 shows the microRNAs that can be identified as being associated with the risk of clinical recurrence while adjusting for the clinical and pathology covariates of biopsy Gleason score, baseline PSA level, and clinical T-stage. The distributions of these covariates are shown in FIG. 1. Fifteen (15) of the microRNAs identified in Table 15 are also present in Table 19, indicating that these microRNAs have predictive value for clinical recurrence that is independent of the Gleason score, baseline PSA, and clinical T-stage.

Two microRNAs assayed from primary Gleason pattern tumor tissue were found that had predictive value for death due to prostate cancer independent of Gleason score, baseline PSA, and clinical T-stage (Table 21).

TABLE 19 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower 95% Bound RM- q-value^(a) Direction Uncorrected Confidence @10% Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p <0.0001 0.0% (−) 1.80 (1.42, 2.27) 1.23 1.53 hsa-miR-30a <0.0001 0.0% (−) 1.75 (1.40, 2.19) 1.22 1.51 hsa-miR-93 <0.0001 0.1% (+) 1.70 (1.32, 2.20) 1.19 1.44 hsa-miR-449a 0.0001 0.1% (+) 1.54 (1.25, 1.91) 1.17 1.39 hsa-miR-133a 0.0001 0.1% (−) 1.58 (1.25, 2.00) 1.17 1.39 hsa-miR-27a 0.0002 0.1% (+) 1.66 (1.28, 2.16) 1.17 1.41 hsa-miR-21 0.0003 0.2% (+) 1.58 (1.23, 2.02) 1.16 1.38 hsa-miR-182 0.0005 0.3% (+) 1.56 (1.22, 1.99) 1.15 1.37 hsa-miR-106b 0.0008 0.5% (+) 1.57 (1.21, 2.05) 1.15 1.36 hsa-miR-222 0.0028 1.1% (−) 1.39 (1.12, 1.73) 1.11 1.28 hsa-miR-103 0.0048 1.7% (+) 1.69 (1.17, 2.43) 1.13 1.32 hsa-miR-486-5p 0.0059 2.0% (−) 1.34 (1.09, 1.65) 1.09 1.25 hsa-miR-1 0.0083 2.7% (−) 1.29 (1.07, 1.57) 1.07 1.23 hsa-miR-141 0.0088 2.8% (+) 1.43 (1.09, 1.87) 1.09 1.27 hsa-miR-200c 0.0116 3.4% (+) 1.39 (1.07, 1.79) 1.07 1.25 hsa-miR-145 0.0201 5.1% (−) 1.27 (1.03, 1.55) 1.05 1.20 hsa-miR-206 0.0329 7.2% (−) 1.40 (1.00, 1.91) 1.05 1.23 hsa-miR-29b 0.0476 9.4% (+) 1.30 (1.00, 1.69) 1.00 1.20 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 20 MicroRNAs Associated with Clinical Recurrence of Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Highest Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower 95% Bound RM- q-value^(a) Direction Uncorrected Confidence @10% Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30a <0.0001 0.0% (−) 1.62 (1.32, 1.99) 1.20 1.43 hsa-miR-30e-5p <0.0001 0.0% (−) 1.53 (1.27, 1.85) 1.19 1.39 hsa-miR-93 <0.0001 0.0% (+) 1.76 (1.37, 2.26) 1.20 1.45 hsa-miR-205 <0.0001 0.0% (−) 1.47 (1.23, 1.74) 1.18 1.36 hsa-miR-449a 0.0001 0.1% (+) 1.62 (1.27, 2.07) 1.18 1.38 hsa-miR-106b 0.0003 0.2% (+) 1.65 (1.26, 2.16) 1.17 1.36 hsa-miR-133a 0.0005 0.2% (−) 1.51 (1.20, 1.90) 1.16 1.33 hsa-miR-1 0.0007 0.3% (−) 1.38 (1.15, 1.67) 1.13 1.28 hsa-miR-210 0.0045 1.2% (+) 1.35 (1.10, 1.67) 1.11 1.25 hsa-miR-182 0.0052 1.3% (+) 1.40 (1.10, 1.77) 1.11 1.26 hsa-miR-425 0.0066 1.6% (+) 1.48 (1.12, 1.96) 1.12 1.26 hsa-miR-155 0.0073 1.8% (−) 1.36 (1.09, 1.70) 1.10 1.24 hsa-miR-21 0.0091 2.1% (+) 1.42 (1.09, 1.84) 1.10 1.25 hsa-miR-222 0.0125 2.7% (−) 1.34 (1.06, 1.69) 1.09 1.23 hsa-miR-27a 0.0132 2.8% (+) 1.40 (1.07, 1.84) 1.09 1.23 hsa-miR-191* 0.0150 3.0% (+) 1.37 (1.06, 1.76) 1.09 1.23 hsa-miR-103 0.0180 3.4% (+) 1.45 (1.06, 1.98) 1.09 1.23 hsa-miR-31 0.0252 4.3% (−) 1.27 (1.00, 1.57) 1.07 1.19 hsa-miR-19b 0.0266 4.5% (−) 1.29 (1.00, 1.63) 1.07 1.20 hsa-miR-99a 0.0310 5.0% (−) 1.26 (1.00, 1.56) 1.06 1.18 hsa-miR-92a 0.0348 5.4% (+) 1.31 (1.00, 1.69) 1.06 1.19 hsa-miR-146b-5p 0.0386 5.8% (−) 1.29 (1.00, 1.65) 1.06 1.19 hsa-miR-145 0.0787 9.7% (−) 1.23 (1.00, 1.55) 1.00 1.15 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

TABLE 21 MicroRNAs Associated with Death Due to Prostate Cancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, and Clinical T-Stage Primary Gleason Pattern Tumor Tissue Absolute Standardized Hazard Ratio Max. Lower 95% Bound RM- q-value^(a) Direction Uncorrected Confidence @10% Corrected MicroRNA p-value (FDR) of Association^(b) Estimate Interval FDR Estimate^(c) hsa-miR-30e-5p 0.0001 2.9% (−) 1.97 (1.40, 2.78) 1.09 1.39 hsa-miR-30a 0.0002 3.3% (−) 1.90 (1.36, 2.65) 1.08 1.38 ^(a)The q-value is the empirical Bayes probability that the microRNA's association with clinical recurrence is a false discovery, given the data. ^(b)Direction of association indicates where higher microRNA expression is associated with higher (+) or lower (−) risk of clinical recurrence. ^(c)RM: regression to the mean.

Accordingly, the normalized expression levels of hsa-miR-93; hsa-miR-106b; hsa-miR-21; hsa-miR-449a; hsa-miR-182; hsa-miR-27a; hsa-miR-103; hsa-miR-141; hsa-miR-92a; hsa-miR-22; hsa-miR-29b; hsa-miR-210; hsa-miR-331; hsa-miR-191; hsa-miR-425; and hsa-miR-200c are positively associated with an increased risk of recurrence; and hsa-miR-30e-5p; hsa-miR-133a; hsa-miR-30a; hsa-miR-222; hsa-miR-1; hsa-miR-145; hsa-miR-486-5p; hsa-miR-19b; hsa-miR-205; hsa-miR-31; hsa-miR-155; hsa-miR-206; hsa-miR-99a; and hsa-miR-146b-5p are negatively associated with an increased risk of recurrence.

Furthermore, the normalized expression levels of hsa-miR-106b; hsa-miR-21; hsa-miR-93; hsa-miR-331; hsa-miR-150; hsa-miR-27b; and hsa-miR-10a are positively associated with an increased risk of prostate cancer specific death; and the normalized expression levels of hsa-miR-30e-5p; hsa-miR-30a; hsa-miR-133a; hsa-miR-222; hsa-miR-1; hsa-miR-26a; and hsa-miR-152 are negatively associated with an increased risk of prostate cancer specific death.

Table 22 shows the number of microRNA-gene pairs that were grouped in each tier (Tiers 1-4) and the number and percentage of those that were predictive of clinical recurrence at a false discovery rate of 10%.

TABLE 22 Number of Pairs Total Number of Predictive of Clinical MicroRNA-Gene Recurrence at False Tier Pairs Discovery Rate 10% (%) Tier 1 80 46 (57.5%) Tier 2 719 591 (82.2%) Tier 3 3,850 2,792 (72.5%) Tier 4 54,724 38,264 (69.9%)

TABLE A SEQ Forward SEQ Reverse SEQ SEQ Official Accession ID Primer ID Primer ID Probe ID Symbol: Number: NO Sequence: NO Sequence: NO Sequence: NO Amplicon Sequence: AAMP NM_001087    1 GTGTGGCAGG    2 CTCCATCCAC    3 CGCTTCAAAGGA    4 GTGTGGCAGGTGGACACTAAGGAGGAGGTCTGGTCCTTTGAA TGGACACTAA TCCAGGTCTC CCAGACCTCCTC GCGGGAGACCTGGAGTGGATGGAG ABCA5 NM_172232    5 GGTATGGATC    6 CAGCCCGCTT    7 CACATGTGGCGA    8 GGTATGGATCCCAAAGCCAAACAGCACATGTGGCGAGCAATT CCAAAGCCA TCTGTTTTTA GCAATTCGAACT CGAACTGCATTTAAAAACAGAAAGCGGGCTG ABCB1 NM_000927    9 AAACACCACT   10 CAAGCCTGGA   11 CAAGCCTGGAAC   12 AAACACCACTGGAGCATTGACTACCAGGCTCGCCAATGATGCT GGAGCATTGA ACCTATAGCC CTATAGCC GCTCAAGTTAAAGGGGCTATAGGTTCCAGGCTTG ABCC1 NM_004996   13 TCATGGTGCC   14 CGATTGTCTT   15 ACCTGATACGTC   16 TCATGGTGCCCGTCAATGCTGTGATGGCGATGAAGACCAAGA CGTCAATG TGCTCTTCAT TTGGTCTTCATC CGTATCAGGTGGCCCACATGAAGAGCAAAGACAATCG GTG GCCAT ABCC3 NM_003786   17 TCATCCTGGC   18 CCGTTGAGTG   19 TCTGTCCTGGCT   20 TCATCCTGGCGATCTACTTCCTCTGGCAGAACCTAGGTCCCTC GATCTACTTC GAATCAGCAA GGAGTCGCTTTC TGTCCTGGCTGGAGTCGCTTTCATGGTCTTGCTGATTCCACTC CT AT AACGG ABCC4 NM_005845   21 AGCGCCTGGA   22 AGAGCCCCTG   23 CGGAGTCCAGTG   24 AGCGCCTGGAATCTACAACTCGGAGTCCAGTGTTTTCCCACTT ATCTACAACT GAGAGAAGAT TTTTCCCACTTA ATCATCTTCTCTCCAGGGGCTCT ABCC8 NM_000352   25 CGTCTGTCAC   26 TGATCCGGTT   27 AGTCTCTTGGCC   28 CGTCTGTCACTGTGGAGTGGACAGGGCTGAAGGTGGCCAAGA TGTGGAGTGG TAGCAGGC ACCTTCAGCCCT GACTGCACCGCAGCCTGCTAAACCGGATCA ABCG2 NM_004827   29 GGTCTCAACG   30 CTTGGATCTT   31 ACGAAGATTTGC   32 GGTCTCAACGCCATCCTGGGACCCACAGGTGGAGGCAAATCT CCATCCTG TCCTTGCAGC CTCCACCTGTGG TCGTTATTAGATGTCTTAGCTGCAAGGAAAGATCCAAG ABHD2 NM_007011   33 GTAGTGGGTC   34 TGAGGGTTGG   35 CAGGTGGCTCCT   36 GTAGTGGGTCTGCATGGATGTTTCAGGGATCAAAGGAGCCAC TGCATGGATG CACTCAGG TTGATCCCTGA CTGGGCGCCTGAGTGCCAACCCTCA T ACE NM_000789   37 CCGCTGTACG   38 CCGTGTCTGT   39 TGCCCTCAGCAA   40 CCGCTGTACGAGGATTTCACTGCCCTCAGCAATGAAGCCTACA AGGATTTCA GAAGCCGT TGAAGCCTACAA AGCAGGACGGCTTCACAGACACGG ACOX2 NM_003500   41 ATGGAGGTGC   42 ACTCCGGGTA   43 TGCTCTCAACTT   44 ATGGAGGTGCCCAGAACACTGCACTCCGCAGGAAAGTTGAGA CCAGAACAC ACTGTGGATG TCCTGCGGAGTG GCATCATCCACAGTTACCCGGAGT ACTR2 NM_005722   45 ATCCGCATTG   46 ATCCGCTAGA   47 CCCGCAGAAAGC   48 ATCCGCATTGAAGACCCACCCCGCAGAAAGCACATGGTATTCC AAGACCCA ACTGCACCAC ACATGGTATTCC TGGGTGGTGCAGTTCTAGCGGAT ADAM15 NM_003815   49 GGCGGGATGT   50 ATTTCTGGGC   51 TCAGCCACAATC   52 GGCGGGATGTGGTAACAGAGACCAAGACTGTGGAGTTGGTGA GGTAACAG CTCCGAGT ACCAACTCCACA TTGTGGCTGATCACTCGGAGGCCCAGAAAT ADAMTS1 NM_006988   53 GGACAGGTGC   54 ATCTACAACC   55 CAAGCCAAAGGC   56 GGACAGGTGCAAGCTCATCTGCCAAGCCAAAGGCATTGGCTA AAGCTCATCT TTGGGCTGCA ATTGGCTACTTC CTTCTTCGTTTTGCAGCCCAAGGTTGTAGAT G A TTCG ADH5 NM_000671   57 ATGCTGTCAT   58 CTGCTTCCTT   59 TGTCTGCCCATT   60 ATGCTGTCATCATTGTCACGGTTTGTCTGCCCATTATCTTCAT CATTGTCACG TCCCTTTCC ATCTTCATTCTG TCTGCAAGGGAAAGGGAAAGGAAGCAG CAA AFAP1 NM_198595   61 GATGTCCATC   62 CAACCCTGAT   63 CCTCCAGTGCTG   64 GATGTCCATCCTTGAAACAGCCTCTTCTGGGAACACAGCACTG CTTGAAACAG GCCTGGAG TGTTCCCAGAAG GAGGTCTCCAGGCATCAGGGTTG C AGTR1 NM_000685   65 AGCATTGATC   66 CTACAAGCAT   67 ATTGTTCACCCA   68 AGCATTGATCGATACCTGGCTATTGTTCACCCAATGAAGTCCC GATACCTGGC TGTGCGTCG ATGAAGTCCCGC GCCTTCGACGCACAATGCTTGTAG AGTR2 NM_000686   69 ACTGGCATAG   70 ATTGACTGGG   71 CCACCCAGACCC   72 ACTGGCATAGGAAATGGTATCCAGAATGGAATTTTGCTACATG GAAATGGTAT TCTCTTTGCC CATGTAGCAAAA GGGTCTGGGTGGGGGCAAAGAGACCCAGTCAAT CC AIG1 NM_016108   73 CGACGGTTCT   74 TGCTCCTGCT   75 AATCGAGATGAG   76 CGACGGTTCTGCCCTTTATATTAATCGAGATGAGGACATCGCA GCCCTTTAT GGGATACTG GACATCGCACCA CCATCAGTATCCCAGCAGGAGCA AKAP1 NM_003488   77 TGTGGTTGGA   78 GTCTACCCAC   79 CTCCACCAGGGA   80 TGTGGTTGGAGATGAAGTGGTGTTGATAAACCGGTCCCTGGTG GATGAAGTGG TGGGCAAGG CCGGTTTATCAA GAGCGAGGCCTTGCCCAGTGGGTAGAC AKR1C1 BC040210   81 GTGTGTGAAG   82 CTCTGCAGGC   83 CCAAATCCCAGG   84 GTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGA CTGAATGATG GCATAGGT ACAGGCATGAAG TTTGGCACCTATGCGCCTGCAGAG G AKR1C3 NM_003739   85 GCTTTGCCTG   86 GTCCAGTCAC   87 TGCGTCACCATC   88 GCTTTGCCTGATGTCTACCAGAAGCCCTGTGTGTGGATGGTGA ATGTCTACCA CGGCATAGAG CACACACAGGG CGCAGAGGACGTCTCTATGCCGGTGACTGGAC GAA A AKT1 NM_005163   89 CGCTTCTATG   90 TCCCGGTACA   91 CAGCCCTGGACT   92 CGCTTCTATGGCGCTGAGATTGTGTCAGCCCTGGACTACCTGC GCGCTGAGAT CCACGTTCTT ACCTGCACTCGG ACTCGGAGAAGAACGTGGTGTACCGGGA AKT2 NM_001626   93 TCCTGCCACC   94 GGCGGTAAAT   95 CAGGTCACGTCC   96 TCCTGCCACCCTTCAAACCTCAGGTCACGTCCGAGGTCGACA CTTCAAACC TCATCATCGA GAGGTCGACACA CAAGGTACTTCGATGATGAATTTACCGCC A AKT3 NM_005465   97 TTGTCTCTGC   98 CCAGCATTAG   99 TCACGGTACACA  100 TTGTCTCTGCCTTGGACTATCTACATTCCGGAAAGATTGTGTA CTTGGACTAT ATTCTCCAAC ATCTTTCCGGA CCGTGATCTCAAGTTGGAGAATCTAATGCTGG CTACA TTGA ALCAM NM_001627  101 GAGGAATATG  102 GTGGCGGAGA  103 CCAGTTCCTGCC  104 GAGGAATATGGAATCCAAGGGGGCCAGTTCCTGCCGTCTGCT GAATCCAAGG TCAAGAGG GTCTGCTCTTCT CTTCTGCCTCTTGATCTCCGCCAC G ALDH18A1 NM_002860  105 GATGCAGCTG  106 CTCCAGCTCA  107 CCTGAAACTTGC  108 GATGCAGCTGGAACCCAAGCTGCAGCAGGAGATGCAAGTTTC GAACCCAA GTGGGGAA ATCTCCTGCTGC AGGATGTTCCCCACTGAGCTGGAG ALDH1A2 NM_170696  109 CACGTCTGTC  110 GACCGTGGCT  111 TCTCTGTAGGGC  112 CACGTCTGTCCCTCTCTGCTTTCTCTGTAGGGCCCAGCTCTCA CCTCTCTGCT CAACTTTGTA CCAGCTCTCAGG GGAATACAAAGTTGAGCCACGGTC T ALKBH3 NM_139178  113 TCGCTTAGTC  114 TCTGAGCCCC  115 TAAACAGGGCAG  116 TCGCTTAGTCTGCACCTCAACCGTGCGGAAAGTGACTGCCCTG TGCACCTCAA AGTTTTTCC TCACTTTCCGCA TTTACTGAGGAAAAACTGGGGCTCAGA C ALOX12 NM_000697  117 AGTTCCTCAA  118 AGCACTAGCC  119 CATGCTGTTGAG  120 AGTTCCTCAATGGTGCCAACCCCATGCTGTTGAGACGCTCGAC TGGTGCCAAC TGGAGGGC ACGCTCGACCTC CTCTCTGCCCTCCAGGCTAGTGCT ALOX5 NM_000698  121 GAGCTGCAGG  122 GAAGCCTGAG  123 CCGCATGCCGTA  124 GAGCTGCAGGACTTCGTGAACGATGTCTACGTGTACGGCATG ACTTCGTGA GACTTGCG CACGTAGACATC CGGGGCCGCAAGTCCTCAGGCTTC AMACR NM_203382  125 GTCTCTGGGC  126 TGGGTATAAG  127 TCCATGTGTTTG  128 GTCTCTGGGCTGTCAGCTTTCCTTTCTCCATGTGTTTGATTTC TGTCAGCTTT ATCCAGAACT ATTTCTCCTCAG TCCTCAGGCTGGTAGCAAGTTCTGGATCTTATACCCA TGC GC AMPD3 NM_000480  129 TGGTTCATCC  130 CATAAATCCG  131 TACTCTCCCAAC  132 TGGTTCATCCAGCACAAGGTCTACTCTCCCAACATGCGCTGGA AGCACAAGG GGGCACCT ATGCGCTGGATC TCATCCAGGTGCCCCGGATTTATG ANGPT2 NM_001147  133 CCGTGAAAGC  134 TTGCAGTGGG  135 AAGCTGACACAG  136 CCGTGAAAGCTGCTCTGTAAAAGCTGACACAGCCCTCCCAAGT TGCTCTGTAA AAGAACAGTC CCCTCCCAAGTG GAGCAGGACTGTTCTTCCCACTGCAA ANLN NM_018685  137 TGAAAGTCCA  138 CAGAACCAAG  139 CCAAAGAACTCG  140 TGAAAGTCCAAAACCAGGAAAATTCCAAAGAACTCGTGTCCCT AAACCAGGAA GCTATCACCA TGTCCCTCGAGC CGAGCTGAATCTGGTGATAGCCTTGGTTCTG ANPEP NM_001150  141 CCACCTTGGA  142 TCTCAGCGTC  143 CTCCCCAACACG  144 CCACCTTGGACCAAAGTAAAGCGTGGAATCGTTACCGCCTCCC CCAAAGTAAA ACCTGGTAGG CTGAAACCCG CAACACGCTGAAACCCGATTCCTACCGGGTGACGCTGAGA GC A ANXA2 NM_004039  145 CAAGACACTA  146 CGTGTCGGGC  147 CCACCACACAGG  148 CAAGACACTAAGGGCGACTACCAGAAAGCGCTGCTGTACCTG AGGGCGACTA TTCAGTCAT TACAGCAGCGCT TGTGGTGGAGATGACTGAAGCCCGACACG CCA APC NM_000038  149 GGACAGCAGG  150 ACCCACTCGA  151 CATTGGCTCCCC  152 GGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCC AATGTGTTTC TTTGTTTCTG GTGACCTGTA AATGGTTCAGAAACAAATCGAGTGGGT APEX1 NM_001641  153 GATGAAGCCT  154 AGGTCTCCAC  155 CTTTCGGGAAGC  156 GATGAAGCCTTTCGCAAGTTCCTGAAGGGCCTGGCTTCCCGAA TTCGCAAGTT ACAGCACAAG CAGGCCCTT AGCCCCTTGTGCTGTGTGGAGACCT APOC1 NM_001645  157 CCAGCCTGAT  158 CACTCTGAAT  159 AGGACAGGACCT  160 CCAGCCTGATAAAGGTCCTGCGGGCAGGACAGGACCTCCCAA AAAGGTCCTG CCTTGCTGGA CCCAACCAAGC CCAAGCCCTCCAGCAAGGATTCAGAGTG APOE NM_000041  161 GCCTCAAGAG  162 CCTGCACCTT  163 ACTGGCGCTGCA  164 GCCTCAAGAGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGC CTGGTTCG CTCCACCA TGTCTTCCAC GCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGG APRT NM_000485  165 GAGGTCCTGG  166 AGGTGCCAGC  167 CCTTAAGCGAGG  168 GAGGTCCTGGAGTGCGTGAGCCTGGTGGAGCTGACCTCGCTT AGTGCGTG TTCTCCCT TCAGCTCCACCA AAGGGCAGGGAGAAGCTGGCACCT AQP2 NM_000486  169 GTGTGGGTGC  170 CCCTTCAGCC  171 CTCCTTCCCTTC  172 GTGTGGGTGCCAGTCCTCCTCAGGAGAAGGGGAAGGGAAGG CAGTCCTC CTCTCAAAG CCCTTCTCCTGA AGGCCACTTTGAGAGGGCTGAAGGG AR NM_000044  173 CGACTTCACC  174 TGACACAAGT  175 ACCATGCCGCCA  176 CGACTTCACCGCACCTGATGTGTGGTACCCTGGCGGCATGGT GCACCTGAT GGGACTGGGA GGGTACCACA GAGCAGAGTGCCCTATCCCAGTCCCACTTGTGTCA TA ARF1 NM_001658  177 CAGTAGAGAT  178 ACAAGCACAT  179 CTTGTCCTTGGG  180 CAGTAGAGATCCCCGCAACTCGCTTGTCCTTGGGTCACCCTGC CCCCGCAACT GGCTATGGAA TCACCCTGCA ATTCCATAGCCATGTGCTTGT ARHGAP29 NM_004815  181 CACGGTCTCG  182 CAGTTGCTTG  183 ATGCCAGACCCA  184 CACGGTCTCGTGGTGAAGTCAATGCCAGACCCAGACAAAGCA TGGTGAAGT CCCAGGAC GACAAAGCATCA TCAGCTTGTCCTGGGCAAGCAACTG ARHGDIB NM_001175  185 TGGTCCCTAG  186 TGATGGAGGA  187 TAAAACCGGGCT  188 TGGTCCCTAGAACAAGAGGCTTAAAACCGGGCTTTCACCCAAC AACAAGAGGC TCAGAGGGAG TTCACCCAACCT CTGCTCCCTCTGATCCTCCATCA ASAP2 NM_003887  189 CGGCCCATCA  190 CTCTGGCCAA  191 CTGGGCTCCAAC  192 CGGCCCATCAGCTTCTACCAGCTGGGCTCCAACCAGCTTCAG GCTTCTAC AGATACAGCG CAGCTTCAGTCT TCTAACGCTGTATCTTTGGCCAGAG ASPN NM_017680  193 TGGACTAATC  194 AAACACCCTT  195 AGTATCACCCAG  196 TGGACTAATCTGTGGGAGCAGTTTATTCCAGTATCACCCAGGG TGTGGGAGCA CAACACAGTC GGTGCAGCCAC TGCAGCCACACCAGGACTGTGTTGAAGGGTGTTT C ATM NM_000051  197 TGCTTTCTAC  198 GTTGTGGATC  199 CCAGCTGTCTTC  200 TGCTTTCTACACATGTTCAGGGATTTTTCACCAGCTGTCTTCG ACATGTTCAG GGCTCGTT GACACTTCTCGC ACACTTCTCGCAAACGAGCCGATCCACAAC GG ATP5E NM_006886  201 CCGCTTTCGC  202 TGGGAGTATC  203 TCCAGCCTGTCT  204 CCGCTTTCGCTACAGCATGGTGGCCTACTGGAGACAGGCTGG TACAGCAT GGATGTAGCT CCAGTAGGCCAC ACTCAGCTACATCCGATACTCCCA G ATP5J NM_  205 GTCGACCGAC  206 CTCTACTTCC  207 CTACCCGCCATC  208 GTCGACCGACTGAAACGGCGGCCCATAATGCATTGCGATGGC 001003703 TGAAACGG GGCCCTGG GCAATGCATTAT GGGTAGGCGTGTGGGGGCGGAGCCAGGGCCGGAAGTAGAG ATXN1 NM_000332  209 GATCGACTCC  210 GAACTGTAT  211 CGGGCTATGGCT  212 GATCGACTCCAGCACCGTAGAGAGGATTGAAGACAGCCATAG AGCACCGTAG CACGGCCACG GTCTTCAATCCT CCCGGGCGTGGCCGTGATACAGTTC AURKA NM_003600  213 CATCTTCCAG  214 TCCGACCTTC  215 CTCTGTGGCACC  216 CATCTTCCAGGAGGACCACTCTCTGTGGCACCCTGGACTACCT GAGGACCACT AATCATTTCA CTGGACTACCTG GCCCCCTGAAATGATTGAAGGTCGGA AURKB NM_004217  217 AGCTGCAGAA  218 GCATCTGCCA  219 TGACGAGCAGCG  220 AGCTGCAGAAGAGCTGCACATTTGACGAGCAGCGAACAGCCA GAGCTGCACA ACTCCTCCAT AACAGCCACG CGATCATGGAGGAGTTGGCAGATGC T AXIN2 NM_004655  221 GGCTATGTCT  222 ATCCGTCAGC  223 ACCAGCGCCAAC  224 GGCTATGTCTTTGCACCAGCCACCAGCGCCAACGACAGTGAG TTGCACCAGC GCATCACT GACAGTGAGATA ATATCCAGTGATGCGCTGACGGAT AZGP1 NM_001185  225 GAGGCCAGCT  226 CAGGAAGGGC  227 TCTGAGATCCCA  228 GAGGCCAGCTAGGAAGCAAGGGTTGGAGGCAATGTGGGATCT AGGAAGCAA AGCTACTGG CATTGCCTCCAA CAGACCCAGTAGCTGCCCTTCCTG BAD NM_032989  229 GGGTCAGGGG  230 CTGCTCACTC  231 TGGGCCCAGAGC  232 GGGTCAGGGGCCTCGAGATCGGGCTTGGGCCCAGAGCATGTT CCTCGAGAT GGCTCAAACT ATGTTCCAGATC CCAGATCCCAGAGTTTGAGCCGAGTGAGCAG C BAG5 NM_  233 ACTCCTGCAA  234 ACAAACAGCT  235 ACACCGGATTTA  236 ACTCCTGCAATGAACCCTGTTGACACCGGATTTAGCTCTTGTC 001015049 TGAACCCTGT CCCCACGA GCTCTTGTCGGC GGCCTTCGTGGGGAGCTGTTTGT BAK1 NM_001188  237 CCATTCCCAC  238 GGGAACATAG  239 ACACCCCAGACG  240 CCATTCCCACCATTCTACCTGAGGCCAGGACGTCTGGGGTGT CATTCTACCT ACCCACCAAT TCCTGGCCT GGGGATTGGTGGGTCTATGTTCCC BAX NM_004324  241 CCGCCGTGGA  242 TTGCCGTCAG  243 TGCCACTCGGAA  244 CCGCCGTGGACACAGACTCCCCCCGAGAGGTCTTTTTCCGAG CACAGACT AAAACATGTC AAAGACCTCTCG TGGCAGCTGACATGTTTTCTGACGGCAA A G BBC3 NM_014417  245 CCTGGAGGGT  246 CTAATTGGGC  247 CATCATGGGACT  248 CCTGGAGGGTCCTGTACAATCTCATCATGGGACTCCTGCCCTT CCTGTACAAT TCCATCTCG CCTGCCCTTACC ACCCAGGGGCCACAGAGCCCCCGAGATGGAGCCCAATTAG BCL2 NM_000633  249 CAGATGGACC  250 CCTATGATTT  251 TTCCACGCCGAA  252 CAGATGGACCTAGTACCCACTGAGATTTCCACGCCGAAGGAC TAGTACCCAC AAGGGCATTT GGACAGCGAT AGCGATGGGAAAAATGCCCTTAAATCATAGG TGAGA TTCC BDKRB1 NM_000710  253 GTGGCAGAAA  254 GAAGGGCAAG  255 ACCTGGCAGCCT  256 GTGGCAGAAATCTACCTGGCCAACCTGGCAGCCTCTGATCTG TCTACCTGGC CCCAAGAC CTGATCTGGTGT GTGTTTGTCTTGGGCTTGCCCTTC BGN NM_001711  257 GAGCTCCGCA  258 CTTGTTGTTC  259 CAAGGGTCTCCA  260 GAGCTCCGCAAGGATGACTTCAAGGGTCTCCAGCACCTCTAC AGGATGAC ACCAGGACGA GCACCTCTACGC GCCCTCGTCCTGGTGAACAACAAG BIK NM_001197  261 ATTCCTATGG  262 GGCAGGAGTG  263 CCGGTTAACTGT  264 ATTCCTATGGCTCTGCAATTGTCACCGGTTAACTGTGGCCTGT CTCTGCAATT AATGGCTCTT GGCCTGTGCCC GCCCAGGAAGAGCCATTCACTCCTGCC GTC C BIN1 NM_004305  265 CCTGCAAAAG  266 CGTGGTTGAC  267 CTTCGCCTCCAG  268 CCTGCAAAAGGGAACAAGAGCCCTTCGCCTCCAGATGGCTCC GGAACAAGAG TCTGATCTCG ATGGCTCCC CCTGCCGCCACCCCCGAGATCAGAGTCAACCACG BIRC5 NM_  269 TTCAGGTGGA  270 CACACAGCAG  271 TCTGCCAGACGC  272 TTCAGGTGGATGAGGAGACAGAATAGAGTGATAGGAAGCGTC 001012271 TGAGGAGACA TGGCAAAAG TTCCTATCACTC TGGCAGATACTCCTTTTGCCACTGCTGTGTG TATTC BMP6 NM_001718  273 GTGCAGACCT  274 CTTAGTTGGC  275 TGAACCCCGAGT  276 GTGCAGACCTTGGTTCACCTTATGAACCCCGAGTATGTCCCCA TGGTTCACCT GCACAGCAC ATGTCCCCAAAC AACCGTGCTGTGCGCCAACTAAG BMPR1B NM_001203  277 ACCACTTTGG  278 GCGGTGTTTG  279 ATTCACATTACC  280 ACCACTTTGGCCATCCCTGCATTTGGGGCCGCTATGGTAATGT CCATCCCT TACCCAGTG ATAGCGGCCCCA GAATGCACTGGGTACAAACACCGC BRCA1 NM_007294  281 TCAGGGGGCT  282 CCATTCCAGT  283 CTATGGGCCCTT  284 TCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACAT AGAAATCTGT TGATCTGTGG CACCAACATGC GCCCACAGATCAACTGGAATGG BRCA2 NM_000059  285 AGTTCGTGCT  286 AAGGTAAGCT  287 CATTCTTCACTG  288 AGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAGCAGTG TTGCAAGATG GGGTCTGCTG CTTCATAAAGCT AAGAATGCAGCAGACCCAGCTTACCTT CTGCA BTG1 NM_001731  289 GAGGTCCGAG  290 AGTTATTTTC  291 CGCTCGTCTCTT  292 GAGGTCCGAGCGATGTGACCAGGCCGCCATCGCTCGTCTCTT CGATGTGA GAGACAGGAG CCTCTCTCCTGC CCTCTCTCCTGCCGCCTCCTGTCTCGAAAATAACT GC BTG3 NM_006806  293 CCATATCGCC  294 CCAGTGATTC  295 CATGGGTACCTC  296 CCATATCGCCCAATTCCAGTGACATGGGTACCTCCTCCTGGAA CAATTCCA CGGTCACAA CTCCTGGAATGC TGCATTGTGACCGGAATCACTGG BTRC NM_033637  297 GTTGGGACAC  298 TGAAGCAGTC  299 CAGTCGGCCCAG  300 GTTGGGACACAGTTGGTCTGCAGTCGGCCCAGGACGGTCTAC AGTTGGTCTG AGTTGTGCTG GACGGTCTACT TCAGCACAACTGACTGCTTCA BUB1 NM_004336  301 CCGAGGTTAA  302 AAGACATGGC  303 TGCTGGGAGCCT  304 CCGAGGTTAATCCAGCACGTATGGGGCCAAGTGTAGGCTCCC TCCAGCACGT GCTCTCAGTT ACACTTGGCCC AGCAGGAACTGAGAGCGCCATGTCTT A C C7 NM_000587  305 ATGTCTGAGT  306 AGGCCTTATG  307 ATGCTCTGCCCT  308 ATGTCTGAGTGTGAGGCGGGCGCTCTGAGATGCAGAGGGCAG GTGAGGCGG CTGGTGACAG CTGCATCTCAGA AGCATCTCTGTCACCAGCATAAGGCCT CACNA1D NM_000720  309 AGGACCCAGC  310 CCTACATTCC  311 CAGTACACTGGC  312 AGGACCCAGCTCCATGTGCGTTCTCAGGGAATGGACGCCAGT TCCATGTG GTGCCATTG GTCCATTCCCTG GTACTGCCAATGGCACGGAATGTAGG CADM1 NM_014333  313 CCACCACCAT  314 GATCCACTGC  315 TCTTCACCTGCT  316 CCACCACCATCCTTACCATCATCACAGATTCCCGAGCAGGTGA CCTTACCATC CCTGATCG CGGGAATCTGTG AGAAGGCTCGATCAGGGCAGTGGATC CADPS NM_003716  317 CAGCAAGGAG  318 GGTCCTCTTC  319 CTCCTGGATGGC  320 CAGCAAGGAGACTGTGCTGAGCTCCTGGATGGCCAAATTTGAT ACTGTGCTGA TCCACGGTAG CAAATTTGATGC GCCATCTACCGTGGAGAAGAGGACC AT CASP1 NM_001223  321 AACTGGAGCT  322 CATCTACGCT  323 TCACAGGCATGA  324 AACTGGAGCTGAGGTTGACATCACAGGCATGACAATGCTGCTA GAGGTTGACA GTACCCCAGA CAATGCTGCTAC CAAAATCTGGGGTACAGCGTAGATG A CASP3 NM_032991  325 TGAGCCTGAG  326 CCTTCCTGCG  327 TCAGCCTGTTCC  328 TGAGCCTGAGCAGAGACATGACTCAGCCTGTTCCATGAAGGC CAGAGACATG TGGTCCAT ATGAAGGCAGAG AGAGCCATGGACCACGCAGGAAGG A C CASP7 NM_033338  329 GCAGCGCCGA  330 AGTCTCTCTC  331 CTTTCGCTAAAG  332 GCAGCGCCGAGACTTTTAGTTTCGCTTTCGCTAAAGGGGCCCC GACTTTTA CGTCGCTCC GGGCCCCAGAC AGACCCTTGCTGCGGAGCGACGGAGAGAGACT CAV1 NM_001753  333 GTGGCTCAAC  334 CAATGGCCTC  335 ATTTCAGCTGAT  336 GTGGCTCAACATTGTGTTCCCATTTCAGCTGATCAGTGGGCCT ATTGTGTTCC CATTTTACAG CAGTGGGCCTCC CCAAGGAGGGGCTGTAAAATGGAGGCCATTG CAV2 NM_198212  337 CTTCCCTGGG  338 CTCCTGGTCA  339 CCCGTACTGTCA  340 CTTCCCTGGGACGACTTGCCAGCTCTGAGGCATGACAGTACG ACGACTTG CCCTTCTGG TGCCTCAGAGCT GGCCCCCAGAAGGGTGACCAGGAG CCL2 NM_002982  341 CGCTCAGCCA  342 GCACTGAGAT  343 TGCCCCAGTCAC  344 CGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT GATGCAATC CTTCCTATTG CTGCTGTTA AACTTCACCAATAGGAAGATCTCAGTGC GTGAA CCL5 NM_002985  345 AGGTTCTGAG  346 ATGCTGACTT  347 ACAGAGCCCTGG  348 AGGTTCTGAGCTCTGGCTTTGCCTTGGCTTTGCCAGGGCTCTG CTCTGGCTTT CCTTCCTGGT CAAAGCCAAG TGACCAGGAAGGAAGTCAGCAT CCNB1 NM_031966  349 TTCAGGTTGT  350 CATCTTCTTG  351 TGTCTCCATTAT  352 TTCAGGTTGTTGCAGGAGACCATGTACATGACTGTCTCCATTA TGCAGGAGAC GGCACACAAT TGATCGGTTCAT TTGATCGGTTCATGCAGAATAATTGTGTGCCCAAGAAGATG GCA CCND1 NM_001758  353 GCATGTTCGT  354 CGGTGTAGAT  355 AAGGAGACCATC  356 GCATGTTCGTGGCCTCTAAGATGAAGGAGACCATCCCCCTGA GGCCTCTAAG GCACAGCTTC CCCCTGACGGC CGGCCGAGAAGCTGTGCATCTACACCG A TC CCNE2 NM_057749  357 ATGCTGTGGC  358 ACCCAAATTG  359 TACCAAGCAACC  360 ATGCTGTGGCTCCTTCCTAACTGGGGCTTTCTTGACATGTAGG TCCTTCCTAA TGATATACAA TACATGTCAAGA TTGCTTGGTAATAACCTTTTTGTATATCACAATTTGGGT CT AAAGGTT AAGCCC CCNH NM_001239  361 GAGATCTTCG  362 CTGCAGACGA  363 CATCAGCGTCCT  364 GAGATCTTCGGTGGGGGTACGGGTGTTTTACGCCAGGACGCT GTGGGGGTA GAACCCAAAC GGCGTAAAACAC GATGCGTTTGGGTTCTCGTCTGCAG CCR1 NM_001295  365 TCCAAGACCC  366 TCGTAGGCTT  367 ACTCACCACACC  368 TCCAAGACCCAATGGGAATTCACTCACCACACCTGCAGCCTTC AATGGGAA TCGTGAGGA TGCAGCCTTCAC ACTTTCCTCACGAAAGCCTACGA CD164 NM_006016  369 CAACCTGTGC  370 ACACCCAAGA  371 CCTCCAATGAAA  372 CAACCTGTGCGAAAGTCTACCTTTGATGCAGCCAGTTTCATTG GAAAGTCTAC CCAGGACAAT CTGGCTGCATCA GAGGAATTGTCCTGGTCTTGGGTGT C CD1A NM_001763  373 GGAGTGGAAG  374 TCATGGGCGT  375 CGCACCATTCGG  376 GGAGTGGAAGGAACTGGAAACATTATTCCGTATACGCACCATT GAACTGGAAA ATCTACGAAT TCATTTGAGG CGGTCATTTGAGGGAATTCGTAGATACGCCCATGA CD276 NM_  377 CCAAAGGATG  378 GGATGACTTG  379 CCACTGTGCAGC  380 CCAAAGGATGCGATACACAGACCACTGTGCAGCCTTATTTCTC 001024736 CGATACACAG GGAATCATGT CTTATTTCTCCA CAATGGACATGATTCCCAAGTCATCC C ATG CD44 NM_000610  381 GGCACCACTG  382 GATGCTCATG  383 ACTGGAACCCAG  384 GGCACCACTGCTTATGAAGGAAACTGGAACCCAGAAGCACAC CTTATGAAGG GTGAATGAGG AAGCACACCCTC CCTCCCCTCATTCACCATGAGCATC CD68 NM_001251  385 TGGTTCCCAG  386 CTCCTCCACC  387 CTCCAAGCCCAG  388 TGGTTCCCAGCCCTGTGTCCACCTCCAAGCCCAGATTCAGATT CCCTGTGT CTGGGTTGT ATTCAGATTCGA CGAGTCATGTACACAACCCAGGGTGGAGGAG GTCA CD82 NM_002231  389 GTGCAGGCTC  390 GACCTCAGGG  391 TCAGCTTCTACA  392 GTGCAGGCTCAGGTGAAGTGCTGCGGCTGGGTCAGCTTCTAC AGGTGAAGTG CGATTCATGA ACTGGACAGACA AACTGGACAGACAACGCTGAGCTCATGAATCGCCCTGAGGTC ACGCTG CDC20 NM_001255  393 TGGATTGGAG  394 GCTTGCACTC  395 ACTGGCCGTGGC  396 TGGATTGGAGTTCTGGGAATGTACTGGCCGTGGCACTGGACA TTCTGGGAAT CACAGGTACA ACTGGACAACA ACAGTGTGTACCTGTGGAGTGCAAGC G CA CDC25B NM_021873  397 GCTGCAGGAC  398 TAGGGCAGCT  399 CTGCTACCTCCC  400 GCTGCAGGACCAGTGAGGGGCCTGCGCCAGTCCTGCTACCTC CAGTGAGG GGCTTCAG TTGCCTTTCGAG CCTTGCCTTTCGAGGCCTGAAGCCAGCTGCCCTA CDC6 NM_001254  401 GCAACACTCC  402 TGAGGGGGAC  403 TTGTTCTCCACC  404 GCAACACTCCCCATTTACCTCCTTGTTCTCCACCAAAGCAAGG CCATTTACCT CATTCTCTTT AAAGCAAGGCAA CAAGAAAGAGAATGGTCCCCCTCA C CDH1 NM_004360  405 TGAGTGTCCC  406 CAGCCGCTTT  407 TGCCAATCCCGA  408 TGAGTGTCCCCCGGTATCTTCCCCGCCCTGCCAATCCCGATGA CCGGTATCTT CAGATTTTCA TGAAATTGGAAA AATTGGAAATTTTATTGATGAAAATCTGAAAGCGGCTG C T TTT CDH10 NM_006727  409 TGTGGTGCAA  410 TGTAAATGAC  411 ATGCCGATGACC  412 TGTGGTGCAAGTCACAGCTACAGATGCCGATGACCCTTCATAT GTCACAGCTA TCTGGCGCTG CTTCATATGGGA GGGAACAGCGCCAGAGTCATTTACA C CDH11 NM_001797  413 GTCGGCAGAA  414 CTACTCATGG  415 CCTTCTGCCCAT  416 GTCGGCAGAAGCAGGACTTGTACCTTCTGCCCATAGTGATCAG GCAGGACT GCGGGATG AGTGATCAGCGA CGATGGCGGCATCCCGCCCATGAGTAG CDH19 NM_021153  417 AGTACCATAA  418 AGACTGCCTG  419 ACTCGGAAAACC  420 AGTACCATAATGCGGGAACGCAAGACTCGGAAAACCACAAGC TGCGGGAACG TATAGGCTCC ACAAGCGCTGAG GCTGAGATCAGGAGCCTATACAGGCAGTCT TG CDH5 NM_001795  421 ACAGGAGACG  422 CAGCAGTGAG  423 TATTCTCCCGGT  424 ACAGGAGACGTGTTCGCCATTGAGAGGCTGGACCGGGAGAAT TGTTCGCC GTGGTACTCT CCAGCCTCTCAA ATCTCAGAGTACCACCTCACTGCTG GA CDH7 NM_033646  425 GTTTGACATG  426 AGTCACATCC  427 ACCTCAACGTCA  428 GTTTGACATGGCTGCACTGAGAAACCTCAACGTCATCCGAGAC GCTGCACTGA CTCCGGGT TCCGAGACACCA ACCAAGACCCGGAGGGATGTGACT CDK14 NM_012395  429 GCAAGGTAAA  430 GATAGCTGTG  431 CTTCCTGCAGCC  432 GCAAGGTAAATGGGAAGTTGGTAGCTCTGAAGGTGATCAGGC TGGGAAGTTG AAAGGTGTCC TGATCACCTTCA TGCAGGAAGAAGAAGGGACACCTTTCACAGCTATC G CT CDK2 NM_001798  433 AATGCTGCAC  434 TTGGTCACAT  435 CCTTGGCCGAAA  436 AATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGC TACGACCCTA CCTGGAAGAA TCCGCTTGT AGCCCTGGCTCACCCTTTCTTCCAGGATGTGACCAA CDK3 NM_001258  437 CCAGGAAGGG  438 GTTGCATGAG  439 CTCTGGCTCCAG  440 CCAGGAAGGGACTGGAAGAGATTGTGCCCAATCTGGAGCCAG ACTGGAAGA CAGGTCCC ATTGGGCACAAT AGGGCAGGGACCTGCTCATGCAAC CDK7 NM_001799  441 GTCTCGGGCA  442 CTCTGGCCTT  443 CCTCCCCAAGGA  444 GTCTCGGGCAAAGCGTTATGAGAAGCTGGACTTCCTTGGGGA AAGCGTTAT GTAAACGGTG AGTCCAGCTTCT GGGACAGTTTGCCACCGTTTACAAGGCCAGAG CDKN1A NM_000389  445 TGGAGACTCT  446 GGCGTTTGGA  447 CGGCGGCAGACC  448 TGGAGACTCTCAGGGTCGAAAACGGCGGCAGACCAGCATGAC CAGGGTCGAA GTGGTAGAAA AGCATGAC AGATTTCTACCACTCCAAACGCC A TC CDKN1C NM_000076  449 CGGCGATCAA  450 CAGGCGCTGA  451 CGGGCCTCTGAT  452 CGGCGATCAAGAAGCTGTCCGGGCCTCTGATCTCCGATTTCTT GAAGCTGT TCTCTTGC CTCCGATTTCTT CGCCAAGCGCAAGAGATCAGCGCCTG CDKN2B NM_004936  453 GACGCTGCAG  454 GCGGGAATCT  455 CACAGGATGCTG  456 GACGCTGCAGAGCACCTTTGCACAGGATGCTGGCCTTTGCTCT AGCACCTT CTCCTCAGT GCCTTTGCTCTT TACTACACTGAGGAGAGATTCCCGC CDKN2C NM_001262  457 GAGCACTGGG  458 CAAAGGCGAA  459 CCTGTAACTTGA  460 GAGCACTGGGCAATCGTTACGACCTGTAACTTGAGGGCCACC CAATCGTTAC CGGGAGTAG GGGCCACCGAAC GAACTGCTACTCCCGTTCGCCTTTG CDKN3 NM_005192  461 TGGATCTCTA  462 ATGTCAGGAG  463 ATCACCCATCAT  464 TGGATCTCTACCAGCAATGTGGAATTATCACCCATCATCATCC CCAGCAATGT TCCCTCCATC CATCCAATCGCA AATCGCAGATGGAGGGACTCCTGACAT G CDS2 NM_003818  465 GGGCTTCTTT  466 ACAGGGCAGA  467 CCCGGACATCAC  468 GGGCTTCTTTGCTACTGTGGTGTTTGGCCTTCTGCTGTCCTAT GCTACTGTGG CAAAGCATCT ATAGGACAGCAG GTGATGTCCGGGTACAGATGCTTTGTCTGCCCTGT CENPF NM_016343  469 CTCCCGTCAA  470 GGGTGAGTCT  471 ACACTGGACCAG  472 CTCCCGTCAACAGCGTTCTTTCCAAACACTGGACCAGGAGTGC CAGCGTTC GGCCTTCA GAGTGCATCCAG ATCCAGATGAAGGCCAGACTCACCC CHAF1A NM_005483  473 GAACTCAGTG  474 GCTCTGTAGC  475 TGCACGTACCAG  476 GAACTCAGTGTATGAGAAGCGGCCTGACTTCAGGATGTGCTG TATGAGAAGC ACCTGCGG CACATCCTGAAG GTACGTGCACCCGCAGGTGCTACAGAGC GG CHN1 NM_001822  477 TTACGACGCT  478 TCTCCCTGAT  479 CCACCATTGGCC  480 TTACGACGCTCGTGAAAGCACATACCACTAAGCGGCCAATGGT CGTGAAAGC GCACATGTCT GCTTAGTGGTAT GGTAGACATGTGCATCAGGGAGA CHRAC1 NM_017444  481 TCTCGCTGCC  482 CCTGGTTGAT  483 ATCCGGGTCATC  484 TCTCGCTGCCTCTATCCCGCATCCGGGTCATCATGAAGAGCTC TCTATCCC GCTGGACA ATGAAGAGCTCC CCCCGAGGTGTCCAGCATCAACCAGG CKS2 NM_001827  485 GGCTGGACGT  486 CGCTGCAGAA  487 CTGCGCCCGCTC  488 GGCTGGACGTGGTTTTGTCTGCTGCGCCCGCTCTTCGCGCTCT GGTTTTGTCT AATGAAACGA TTCGCG CGTTTCATTTTCTGCAGCG CLDN3 NM_001306  489 ACCAACTGCG  490 GGCGAGAAGG  491 CAAGGCCAAGAT  492 ACCAACTGCGTGCAGGACGACACGGCCAAGGCCAAGATCACC TGCAGGAC AACAGCAC CACCATCGTGG ATCGTGGCAGGCGTGCTGTTCCTTCTCGCC CLTC NM_004859  493 ACCGTATGGA  494 TGACTACAGG  495 TCTCACATGCTG  496 ACCGTATGGACAGCCACAGCCTGGCTTTGGGTACAGCATGTG CAGCCACAG ATCAGCGCTT TACCCAAAGCCA AGATGAAGCGCTGATCCTGTAGTCA C COL11A1 NM_001854  497 GCCCAAGAGG  498 GGACCTGGGT  499 CTGCTCGACCTT  500 GCCCAAGAGGGGAAGATGGCCCTGAAGGACCCAAAGGTCGA GGAAGATG CTCCAGTTG TGGGTCCTTCAG GCAGGCCCAACTGGAGACCCAGGTCC COL1A1 NM_000088  501 GTGGCCATCC  502 CAGTGGTAGG  503 TCCTGCGCCTGA  504 GTGGCCATCCAGCTGACCTTCCTGCGCCTGATGTCCACCGAG AGCTGACC TGATGTTCTG TGTCCACCG GCCTCCCAGAACATCACCTACCACTG GGA COL1A2 NM_000089  505 CAGCCAAGAA  506 AAACTGGCTG  507 TCTCCTAGCCAG  508 CAGCCAAGAACTGGTATAGGAGCTCCAAGGACAAGAAACACG CTGGTATAGG CCAGCATTG ACGTGTTTCTTG TCTGGCTAGGAGAAACTATCAATGCTGGCAGCCAGTTT AGCT TCCTTG COL3A1 NM_000090  509 GGAGGTTCTG  510 ACCAGGACTG  511 CTCCTGGTCCCC  512 GGAGGTTCTGGACCTGCTGGTCCTCCTGGTCCCCAAGGTGTC GACCTGCTG CCACGTTC AAGGTGTCAAAG AAAGGTGAACGTGGCAGTCCTGGT COL4A1 NM_001845  513 ACAAAGGCCT  514 GAGTCCCAGG  515 CTCCTTTGACAC  516 ACAAAGGCCTCCCAGGATTGGATGGCATCCCTGGTGTCAAAG CCCAGGAT AAGACCTGCT CAGGGATGCCAT GAGAAGCAGGTCTTCCTGGGACTC COL5A1 NM_000093  517 CTCCCTGGGA  518 CTGGACCAGG  519 CCAGGGAAACCA  520 CTCCCTGGGAAAGATGGCCCTCCAGGATTACGTGGTTTCCCTG AAGATGGC AAGCCCTC CGTAATCCTGGA GGGACCGAGGGCTTCCTGGTCCAG COL5A2 NM_000393  521 GGTCGAGGAA  522 GCCTGGAGGT  523 CCAGGAAATCCT  524 GGTCGAGGAACCCAAGGTCCGCCTGGTGCTACAGGATTTCCT CCCAAGGT CCAACTCTG GTAGCACCAGGC GGTTCTGCGGGCAGAGTTGGACCTCCAGGC COL6A1 NM_001848  525 GGAGACCCTG  526 TCTCCAGGGA  527 CTTCTCTTCCCT  528 GGAGACCCTGGTGAAGCTGGCCCGCAGGGTGATCAGGGAAG GTGAAGCTG CACCAACG GATCACCCTGCG AGAAGGCCCCGTTGGTGTCCCTGGAGA COL6A3 NM_004369  529 GAGAGCAAGC  530 AACAGGGAAC  531 CCTCTTTGACGG  532 GAGAGCAAGCGAGACATTCTGTTCCTCTTTGACGGCTCAGCCA GAGACATTCT TGGCCCAC CTCAGCCAATCT ATCTTGTGGGCCAGTTCCCTGTT G COL8A1 NM_001850  533 TGGTGTTCCA  534 CCCTGTAAAC  535 CCTAAGGGAGAG  536 TGGTGTTCCAGGGCTTCTCGGACCTAAGGGAGAGCCAGGAAT GGGCTTCT CCTGATCCC CCAGGAATCCCA CCCAGGGGATCAGGGTTTACAGGG COL9A2 NM_001852  537 GGGAACCATC  538 ATTCCGGGTG  539 ACACAGGAAATC  540 GGGAACCATCCAGGGTCTGGAAGGCAGTGCGGATTTCCTGTG CAGGGTCT GACAGTTG CGCACTGCCTTC TCCAACCAACTGTCCACCCGGAAT CRISP3 NM_006061  541 TCCCTTATGA  542 AACCATTGGT  543 TGCCAGTTGCCC  544 TCCCTTATGAACAAGGAGCACCTTGTGCCAGTTGCCCAGATAA ACAAGGAGCA GCATAGTCCA AGATAACTGTGA CTGTGACGATGGACTATGCACCAATGGTT C T CSF1 NM_000757  545 TGCAGCGGCT  546 CAACTGTTCC  547 TCAGATGGAGAC  548 TGCAGCGGCTGATTGACAGTCAGATGGAGACCTCGTGCCAAA GATTGACA TGGTCTACAA CTCGTGCCAAAT TTACATTTGAGTTTGTAGACCAGGAACAGTTG ACTCA TACA CSK NM_004383  549 CCTGAACATG  550 CATCACGTCT  551 TCCCGATGGTCT  552 CCTGAACATGAAGGAGCTGAAGCTGCTGCAGACCATCGGGAA AAGGAGCTGA CCGAACTCC GCAGCAGCT GGGGGAGTTCGGAGACGTGATG CSRP1 NM_004078  553 ACCCAAGACC  554 GCAGGGGTGG  555 CCACCCTTCTCC  556 ACCCAAGACCCTGCCTCTTCCACTCCACCCTTCTCCAGGGACC CTGCCTCT AGTGATGT AGGGACCCTTAG CTTAGATCACATCACTCCACCCCTGC CTGF NM_001901  557 GAGTTCAAGT  558 AGTTGTAATG  559 AACATCATGTTC  560 GAGTTCAAGTGCCCTGACGGCGAGGTCATGAAGAAGAACATG GCCCTGACG GCAGGCACAG TTCTTCATGACC ATGTTCATCAAGACCTGTGCCTGCCATTACAACT TCGC CTHRC1 NM_138455  561 TGGCTCACTT  562 TCAGCTCCAT  563 CAACGCTGACAG  564 TGGCTCACTTCGGCTAAAATGCAGAAATGCATGCTGTCAGCGT CGGCTAAAAT TGAATGTGAA CATGCATTTCTG TGGTATTTCACATTCAATGGAGCTGA A CTNNA1 NM_001903  565 CGTTCCGATC  566 AGGTCCCTGT  567 ATGCCTACAGCA  568 CGTTCCGATCCTCTATACTGCATCCCAGGCATGCCTACAGCAC CTCTATACTG TGGCCTTATA CCCTGATGTCGC CCTGATGTCGCAGCCTATAAGGCCAACAGGGACCT CAT GG A CTNNB1 NM_001904  569 GGCTCTTGTG  570 TCAGATGACG  571 AGGCTCAGTGAT  572 GGCTCTTGTGCGTACTGTCCTTCGGGCTGGTGACAGGGAAGA CGTACTGTCC AAGAGCACAG GTCTTCCCTGTC CATCACTGAGCCTGCCATCTGTGCTCTTCGTCATCTGA TT ATG ACCAG CTNND1 NM_001331  573 CGGAAACTTC  574 CTGAATCCTT  575 TTGATGCCCTCA  576 CGGAAACTTCGGGAATGTGATGGTTTAGTTGATGCCCTCATTT GGGAATGTGA CTGCCCAATC TTTTCATTGTTC TCATTGTTCAGGCTGAGATTGGGCAGAAGGATTCAG TC AGGC CTNND2 NM_001332  577 GCCCGTCCCT  578 CTCACACCCA  579 CTATGAAACGAG  580 GCCCGTCCCTACAGTGAACTGAACTATGAAACGAGCCACTACC ACAGTGAAC GGAGTCGG CCACTACCCGGC CGGCCTCCCCCGACTCCTGGGTGTGAG CTSB NM_001908  581 GGCCGAGATC  582 GCAGGAAGTC  583 CCCCGTGGAGGG  584 GGCCGAGATCTACAAAAACGGCCCCGTGGAGGGAGCTTTCTC TACAAAAACG CGAATACACA AGCTTTCTC TGTGTATTCGGACTTCCTGC CTSD NM_001909  585 GTACATGATC  586 GGGACAGCTT  587 ACCCTGCCCGCG  588 GTACATGATCCCCTGTGAGAAGGTGTCCACCCTGCCCGCGAT CCCTGTGAGA GTAGCCTTTG ATCACACTGA CACACTGAAGCTGGGAGGCAAAGGCTACAAGCTGTCCC AGGT C CTSK NM_000396  589 AGGCTTCTCT  590 CCACCTCTTC  591 CCCCAGGTGGTT  592 AGGCTTCTCTTGGTGTCCATACATATGAACTGGCTATGAACCA TGGTGTCCAT ACTGGTCATG CATAGCCAGTTC CCTGGGGGACATGACCAGTGAAGAGGTGG AC T CTSL2 NM_001333  593 TGTCTCACTG  594 ACCATTGCAG  595 CTTGAGGACGCG  596 TGTCTCACTGAGCGAGCAGAATCTGGTGGACTGTTCGCGTCCT AGCGAGCAGA CCCTGATTG AACAGTCCACCA CAAGGCAATCAGGGCTGCAATGGT A CTSS NM_004079  597 TGACAACGGC  598 TCCATGGCTT  599 TGATAACAAGGG  600 TGACAACGGCTTTCCAGTACATCATTGATAACAAGGGCATCGA TTTCCAGTAC TGTAGGGATA CATCGACTCAGA CTCAGACGCTTCCTATCCCTACAAAGCCATGGA AT GG CGCT CUL1 NM_003592  601 ATGCCCTGGT  602 GCGACCACAA  603 CAGCCACAAAGC  604 ATGCCCTGGTAATGTCTGCATTCAACAATGACGCTGGCTTTGT AATGTCTGCA GCCTTATCAA CAGCGTCATTGT GGCTGCTCTTGATAAGGCTTGTGGTCGC T G CXCL12 NM_000609  605 GAGCTACAGA  606 TTTGAGATGC  607 TTCTTCGAAAGC  608 GAGCTACAGATGCCCATGCCGATTCTTCGAAAGCCATGTTGCC TGCCCATGC TTGACGTTGG CATGTTGCCAGA AGAGCCAACGTCAAGCATCTCAAA CXCR4 NM_003467  609 TGACCGCTTC  610 AGGATAAGGC  611 CTGAAACTGGAA  612 TGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAG TACCCCAATG CAACCATGAT CACAACCACCCA TTTCAGCACATCATGGTTGGCCTTATCCT GT CAAG CXCR7 NM_020311  613 CGCCTCAGAA  614 GTTGCATGGC  615 CTCAGAGCCAGG  616 CGCCTCAGAACGATGGATCTGCATCTCTTCGACTACTCAGAGC CGATGGAT CAGCTGAT GAACTTCTCGGA CAGGGAACTTCTCGGACATCAGCTGGCCATGCAAC CYP3A5 NM_000777  617 TCATTGCCCA  618 GACAGGCTTG  619 TCCCGCCTCAAG  620 TCATTGCCCAGTATGGAGATGTATTGGTGAGAAACTTGAGGCG GTATGGAGAT CCTTTCTCTG TTTCTCACCAAT GGAAGCAGAGAAAGGCAAGCCTGTC G CYR61 NM_001554  621 TGCTCATTCT  622 GTGGCTGCAT  623 CAGCACCCTTGG  624 TGCTCATTCTTGAGGAGCATTAAGGTATTTCGAAACTGCCAAG TGAGGAGCAT TAGTGTCCAT CAGTTTCGAAAT GGTGCTGGTGCGGATGGACACTAATGCAGCCAC DAG1 NM_004393  625 GTGACTGGGC  626 ATCCCACTTG  627 CAAGTCAGAGTT  628 GTGACTGGGCTCATGCCTCCAAGTCAGAGTTTCCCTGGTGCC TCATGCCT TGCTCCTGTC TCCCTGGTGCCC CCAGAGACAGGAGCACAAGTGGGAT DAP NM_004394  629 CCAGCCTTTC  630 GACCAGGTCT  631 CTCACCAGCTGG  632 CCAGCCTTTCTGGTGCTGTTCTCCAGTTCACGTCTGCCAGCTG TGGTGCTG GCCTCTGC CAGACGTGAACT GTGAGGGCAGAGGCAGACCTGGTC DAPK1 NM_004938  633 CGCTGACATC  634 TCTCTTTCAG  635 TCATATCCAAAC  636 CGCTGACATCATGAATGTTCCTCGACCGGCTGGAGGCGAGTTT ATGAATGTTC CAACGATGTG TCGCCTCCAGCC GGATATGACAAAGACACATCGTTGCTGAAAGAGA CT TCTT G DARC NM_002036  637 GCCCTCATTA  638 CAGACAGAAG  639 TCAGCGCCTGTG  640 GCCCTCATTAGTCCTTGGCTCTTATCTTGGAAGCACAGGCGCT GTCCTTGGCT GGCTGGGAC CTTCCAAGATAA GACAGCCGTCCCAGCCCTTCTGTCTG DDIT4 NM_019058  641 CCTGGCGTCT  642 CGAAGAGGAG  643 CTAGCCTTTGGG  644 CCTGGCGTCTGTCCTCACCATGCCTAGCCTTTGGGACCGCTTC GTCCTCAC GTGGACGA ACCGCTTCTCGT TCGTCGTCGTCCACCTCCTCTTCG DDR2 NM_  645 CTATTACCGG  646 CCCAGCAAGA  647 AGTGCTCCCTAT  648 CTATTACCGGATCCAGGGCCGGGCAGTGCTCCCTATCCGCTG 001014796 ATCCAGGGC TACTCTCCCA CCGCTGGATGTC GATGTCTTGGGAGAGTATCTTGCTGGG DES NM_001927  649 ACTTCTCACT  650 GCTCCACCTT  651 TGAACCAGGAGT  652 ACTTCTCACTGGCCGACGCGGTGAACCAGGAGTTTCTGACCA GGCCGACG CTCGTTGGT TTCTGACCACGC CGCGCACCAACGAGAAGGTGGAGC DHRS9 NM_005771  653 GGAGAAAGGT  654 CAGTCAGTGG  655 ATCAATAATGCT  656 GGAGAAAGGTCTCTGGGGTCTGATCAATAATGCTGGTGTTCCC CTCTGGGGTC GAGCCAGC GGTGTTCCCGGC GGCGTGCTGGCTCCCACTGACTG DHX9 NM_001357  657 GTTCGAACCA  658 TCCAGTTGGA  659 CCAAGGAACCAC  660 GTTCGAACCATCTCAGCGACAAAACCAAGTGGGTGTGGTTCCT TCTCAGCGAC TTGTGGAGGT ACCCACTTGGTT TGGTCACCTCCACAATCCAACTGGA DIAPH1 NM_005219  661 CAAGCAGTCA  662 AGTTTTGCTC  663 TTCTTCTGTCTC  664 CAAGCAGTCAAGGAGAACCAGAAGCGGCGGGAGACAGAAGA AGGAGAACCA GCCTCATCTT CCGCCGCTTC AAAGATGAGGCGAGCAAAACT DICER1 NM_177438  665 TCCAATTCCA  666 GGCAGTGAAG  667 AGAAAAGCTGTT  668 TCCAATTCCAGCATCACTGTGGAGAAAAGCTGTTTGTCTCCCC GCATCACTGT GCGATAAAGT TGTCTCCCCAGC AGCATACTTTATCGCCTTCACTGCC A DIO2 NM_013989  669 CTCCTTTCAC  670 AGGAAGTCAG  671 ACTCTTCCACCA  672 CTCCTTTCACGAGCCAGCTGCCAGCCTTCCGCAAACTGGTGG GAGCCAGC CCACTGAGGA GTTTGCGGAAGG AAGAGTTCTCCTCAGTGGCTGACTTCCT DLC1 NM_006094  673 GATTCAGACG  674 CACCTCTTGC  675 AAAGTCCATTTG  676 GATTCAGACGAGGATGAGCCTTGTGCCATCAGTGGCAAATGG AGGATGAGCC TGTCCCTTTG CCACTGATGGCA ACTTTCCAAAGGGACAGCAAGAGGTG DLGAP1 NM_004746  677 CTGCTGAGCC  678 AGCCTGGAAG  679 CGCAGACCACCC  680 CTGCTGAGCCCAGTGGAGCACCACCCCGCAGACCACCCATAC CAGTGGAG GAGTTCCG ATACTACACCCA TACACCCAGCGGAACTCCTTCCAGGCT DLL4 NM_019074  681 CACGGAGGTA  682 AGAAGGAAGG  683 CTACCTGGACAT  684 CACGGAGGTATAAGGCAGGAGCCTACCTGGACATCCCTGCTC TAAGGCAGGA TCCAGCCG CCCTGCTCAGCC AGCCCCGCGGCTGGACCTTCCTTCT G DNM3 NM_015569  685 CTTTCCCACC  686 AAGGACCTTC  687 CATATCGCTGAC  688 CTTTCCCACCCGGCTTACAGACATATCGCTGACCGAATGGGAA CGGCTTAC TGCAGGTGTG CGAATGGGAACC CCCCACACCTGCAGAAGGTCCTT DPP4 NM_001935  689 GTCCTGGGAT  690 GTACTCCCAC  691 CGGCTATTCCAC  692 GTCCTGGGATCGGGAAGTGGCGTGTTCAAGTGTGGAATAGCC CGGGAAGT CGGGATACAG ACTTGAACACGC GTGGCGCCTGTATCCCGGTGGGAGTAC DPT NM_001937  693 CACCTAGAAG  694 CAGTAGCTCC  695 TTCCTAGGAAGG  696 CACCTAGAAGCCTGCCCACGATTCCTAGGAAGGCTGGCAGAC CCTGCCCAC CCAGGGTTC CTGGCAGACACC ACCCTGGAACCCTGGGGAGCTACTG DUSP1 NM_004417  697 AGACATCAGC  698 GACAAACACC  699 CGAGGCCATTGA  700 AGACATCAGCTCCTGGTTCAACGAGGCCATTGACTTCATAGAC TCCTGGTTCA CTTCCTCCAG CTTCATAGACTC TCCATCAAGAATGCTGGAGGAAGGGTGTTTGTC CA DUSP6 NM_001946  701 CATGCAGGGA  702 TGCTCCTACC  703 TCTACCCTATGC  704 CATGCAGGGACTGGGATTCGAGGACTTCCAGGCGCATAGGGT CTGGGATT CTATCATTTG GCCTGGAAGTCC AGAACCAAATGATAGGGTAGGAGCA G DVL1 NM_004421  705 TCTGTCCCAC  706 TCAGACTGTT  707 CTTGGAGCAGCC  708 TCTGTCCCACCTGCTGCTGCCCCTTGGAGCAGCCTGCACCTTC CTGCTGCT GCCGGATG TGCACCTTCTCT TCTCCTCCCATCCGGCAACAGTCTGA DYNLL1 NM_  709 GCCGCCTACC  710 GCCTGACTCC  711 ACCCACGTCAGT  712 GCCGCCTACCTCACAGACTTGTGAGCACTCACTGACGTGGGT 001037494 TCACAGAC AGCTCTCCT GAGTGCTCACAA AGCGCCCAGGGCCTGCGGGGCGCAGGAGAGCTGGAGTCAGG C EBNA1BP2 NM_006824  713 TGCGGCGAGA  714 GTGACAAGGG  715 CCCGCTCTCGGA  716 TGCGGCGAGATGGACACTCCCCCGCTCTCGGATTCGGAGTCG TGGACACT ATTCATCGGA TTCGGAGTCG GAATCCGATGAATCCCTTGTCAC TT ECE1 NM_001397  717 ACCTTGGGAT  718 GGACCAGGAC  719 TCCACTCTCGAT  720 ACCTTGGGATCTGCCTCCAAGCTGGTGCAGGGTATCGAGAGT CTGCCTCC CTCCATCTG ACCCTGCACCAG GGATTCCAGATGGAGGTCCTGGTCC EDN1 NM_001955  721 TGCCACCTGG  722 TGGACCTAGG  723 CACTCCCGAGCA  724 TGCCACCTGGACATCATTTGGGTCAACACTCCCGAGCACGTTG ACATCATTTG GCTTCCAAGT CGTTGTTCCGT TTCCGTATGGACTTGGAAGCCCTAGGTCCA C EDNRA NM_001957  725 TTTCCTCAAA  726 TTACACATCC  727 CCTTTGCCTCAG  728 TTTCCTCAAATTTGCCTCAAGATGGAAACCCTTTGCCTCAGGG TTTGCCTCAA AACCAGTGCC GGCATCCTTTT CATCCTTTTGGCTGGCACTGGTTGGATGTGTAA G EFNB2 NM_004093  729 TGACATTATC  730 GTAGTCCCCG  731 CGGACAGCGTCT  732 TGACATTATCATCCCGCTAAGGACTGCGGACAGCGTCTTCTGC ATCCCGCTAA CTGACCTTCT TCTGCCCTCACT CCTCACTACGAGAAGGTCAGCGGGGACTAC GGA C EGF NM_001963  733 CTTTGCCTTG  734 AAATACCTGA  735 AGAGTTTAACAG  736 CTTTGCCTTGCTCTGTCACAGTGAAGTCAGCCAGAGCAGGGCT CTCTGTCACA CACCCTTATG CCCTGCTCTGGC GTTAAACTCTGTGAAATTTGTCATAAGGGTGTCAGGTATTT GT ACAAATT TGACTT EGR1 NM_001964  737 GTCCCCGCTG  738 CTCCAGCTTA  739 CGGATCCTTTCC  740 GTCCCCGCTGCAGATCTCTGACCCGTTCGGATCCTTTCCTCAC CAGATCTCT GGGTAGTTGT TCACTCGCCCA TCGCCCACCATGGACAACTACCCTAAGCTGGAG CCAT EGR3 NM_004430  741 CCATGTGGAT  742 TGCCTGAGAA  743 ACCCAGTCTCAC  744 CCATGTGGATGAATGAGGTGTCTCCTTTCCATACCCAGTCTCA GAATGAGGTG GAGGTGAGGT CTTCTCCCCACC CCTTCTCCCCACCCTACCTCACCTCTTCTCAGGCA EIF2C2 NM_012154  745 GCACTGTGGG  746 ATGTTTGGTG  747 CGGGTCACATTG  748 GCACTGTGGGCAGATGAAGAGGAAGTACCGCGTCTGCAATGT CAGATGAA ACTGGCGG CAGACACGGTAC GACCCGGCGGCCCGCCAGTCACCAAACAT EIF2S3 NM_001415  749 CTGCCTCCCT  750 GGTGGCAAGT  751 TCTCGTGCTTCA  752 CTGCCTCCCTGATTCAAGTGATTCTCGTGCTTCAGCCTCCCAT GATTCAAGTG GCCTGTAATA GCCTCCCATGTA GTAGCTGATATTACAGGCACTTGCCACC TC EIF3H NM_003756  753 CTCATTGCAG  754 GCCATGAAGA  755 CAGAACATCAAG  756 CTCATTGCAGGCCAGATAAACACTTACTGCCAGAACATCAAGG GCCAGATAAA GCTTGCCTA GAGTTCACTGCC AGTTCACTGCCCAAAACTTAGGCAAGCTCTTCATGGC CA EIF4E NM_001968  757 GATCTAAGAT  758 TTAGATTCCG  759 ACCACCCCTACT  760 GATCTAAGATGGCGACTGTCGAACCGGAAACCACCCCTACTC GGCGACTGTC TTTTCTCCTC CCTAATCCCCCG CTAATCCCCCGACTACAGAAGAGGAGAAAACGGAATCTAA GAA TTCTG ACT EIF5 NM_001969  761 GAATTGGTCT  762 TCCAGGTATA  763 CCACTTGCACCC  764 GAATTGGTCTCCAGCTGCCTTTGATCAAGATTCGGGTGCAAGT CCAGCTGCC TGGCTCCTGC GAATCTTGATCA GGAGCAGGAGCCATATACCTGGA ELK4 NM_001973  765 GATGTGGAGA  766 AGTCATTGCG  767 ATAAACCACCTC  768 GATGTGGAGAATGGAGGGAAAGATAAACCACCTCAGCCTGGT ATGGAGGGAA GCTAGAGGTC AGCCTGGTGCCA GCCAAGACCTCTAGCCGCAATGACT ENPP2 NM_006209  769 CTCCTGCGCA  770 TCCCTGGATA  771 TAACTTCCTCTG  772 CTCCTGCGCACTAATACCTTCAGGCCAACCATGCCAGAGGAA CTAATACCTT ATTGGGTCTG GCATGGTTGGCC GTTACCAGACCCAATTATCCAGGGA C ENY2 NM_020189  773 CCTCAAAGAG  774 CCTCTTTACA  775 CTGATCCTTCCA  776 CCTCAAAGAGTTGCTGAGAGCTAAATTAATTGAATGTGGCTGG TTGCTGAGAG GTGTGCCTTC GCCACATTCAAT AAGGATCAGTTGAAGGCACACTGTAAAGAGG C A TAATTT EPHA2 NM_004431  777 CGCCTGTTCA  778 GTGGCGTGCC  779 TGCGCCCGATGA  780 CGCCTGTTCACCAAGATTGACACCATTGCGCCCGATGAGATCA CCAAGATTGA TCGAAGTC GATCACCG CCGTCAGCAGCGACTTCGAGGCACGCCAC C EPHA3 NM_005233  781 CAGTAGCCTC  782 TTCGTCCCAT  783 TATTCCAAATCC  784 CAGTAGCCTCAAGCCTGACACTATATACGTATTCCAAATCCGA AAGCCTGACA ATCCAGCG GAGCCCGAACAG GCCCGAACAGCCGCTGGATATGGGACGAA EPHB2 NM_004442  785 CAACCAGGCA  786 GTAATGCTGT  787 CACCTGATGCAT  788 CAACCAGGCAGCTCCATCGGCAGTGTCCATCATGCATCAGGT GCTCCATC CCACGGTGC GATGGACACTGC GAGCCGCACCGTGGACAGCATTAC EPHB4 NM_004444  789 TGAACGGGGT  790 AGGTACCTCT  791 CGTCCCATTTGA  792 TGAACGGGGTATCCTCCTTAGCCACGGGGCCCGTCCCATTTG ATCCTCCTTA CGGTCAGTGG GCCTGTCAATGT AGCCTGTCAATGTCACCACTGACCGAGAGGTACCT ERBB2 NM_004448  793 CGGTGTGAGA  794 CCTCTCGCAA  795 CCAGACCATAGC  796 CGGTGTGAGAAGTGCAGCAAGCCCTGTGCCCGAGTGTGCTAT AGTGCAGCAA GTGCTCCAT ACACTCGGGCAC GGTCTGGGCATGGAGCACTTGCGAGAGG ERBB3 NM_001982  797 CGGTTATGTC  798 GAACTGAGAC  799 CCTCAAAGGTAC  800 CGGTTATGTCATGCCAGATACACACCTCAAAGGTACTCCCTCC ATGCCAGATA CCACTGAAGA TCCCTCCTCCCG TCCCGGGAAGGCACCCTTTCTTCAGTGGGTCTCAGTTC CAC AAGG G ERBB4 NM_005235  801 TGGCTCTTAA  802 CAAGGCATAT  803 TGTCCCACGAAT  804 TGGCTCTTAATCAGTTTCGTTACCTGCCTCTGGAGAATTTACG TCAGTTTCGT CGATCCTCAT AATGCGTAAATT CATTATTCGTGGGACAAAACTTTATGAGGATCGATATGCCTTG TACCT AAAGT CTCCAG ERCC1 NM_001983  805 GTCCAGGTGG  806 CGGCCAGGAT  807 CAGCAGGCCCTC  808 GTCCAGGTGGATGTGAAAGATCCCCAGCAGGCCCTCAAGGAG ATGTGAAAGA ACACATCTTA AAGGAGCTG CTGGCTAAGATGTGTATCCTGGCCG EREG NM_001432  809 TGCTAGGGTA  810 TGGAGACAAG  811 TAAGCCATGGCT  812 TGCTAGGGTAAACGAAGGCATAATAAGCCATGGCTGACCTCTG AACGAAGGCA TCCTGGCAC GACCTCTGGAGC GAGCACCAGGTGCCAGGACTTGTCTCCA ERG NM_004449  813 CCAACACTAG  814 CCTCCGCCAG  815 AGCCATATGCCT  816 CCAACACTAGGCTCCCCACCAGCCATATGCCTTCTCATCTGGG GCTCCCCA GTCTTTAGT TCTCATCTGGGC CACTTACTACTAAAGACCTGGCGGAGG ESR1 NM_000125  817 CGTGGTGCCC  818 GGCTAGTGGG  819 CTGGAGATGCTG  820 CGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGC CTCTATGAC CGCATGTAG GACGCCC CCACCGCCTACATGCGCCCACTAGCC ESR2 NM_001437  821 TGGTCCATCG  822 TGTTCTAGCG  823 ATCTGTATGCGG  824 TGGTCCATCGCCAGTTATCACATCTGTATGCGGAACCTCAAAA CCAGTTATCA ATCTTGCTTC AACCTCAAAAGA GAGTCCCTGGTGTGAAGCAAGATCGCTAGAACA ACA GTCCCT ETV1 NM_004956  825 TCAAACAAGA  826 AACTGCCAGA  827 ATCGGGAAGGAC  828 TCAAACAAGAGCCAGGAATGTATCGGGAAGGACCCACATACC GCCAGGAATG GCTGAAGTGA CCACATACCAAC AACGGCGAGGATCACTTCAGCTCTGGCAGTT ETV4 NM_001986  829 TCCAGTGCCT  830 ACTGTCCAAG  831 CAGACAAATCGC  832 TCCAGTGCCTATGACCCCCCCAGACAAATCGCCATCAAGTCCC ATGACCCC GGCACCAG CATCAAGTCCCC CTGCCCCTGGTGCCCTTGGACAGT EZH2 NM_004456  833 TGGAAACAGC  834 CACCGAACAC  835 TCCTGACTTCTG  836 TGGAAACAGCGAAGGATACAGCCTGTGCACATCCTGACTTCTG GAAGGATACA TCCCTAGTCC TGAGCTCATTGC TGAGCTCATTGCGCGGGACTAGGGAGTGTTCGGTG G F2R NM_001992  837 AAGGAGCAAA  838 GCAGGGTTTC  839 CCCGGGCTCAAC  840 AAGGAGCAAACCATCCAGGTGCCCGGGCTCAACATCACTACC CCATCCAGG ATTGAGCAC ATCACTACCTGT TGTCATGATGTGCTCAATGAAACCCTGC FAAH NM_001441  841 GACAGCGTAG  842 AGCTGAACAT  843 TGCCCTTCGTGC  844 GACAGCGTAGTGGTGCATGTGCTGAAGCTGCAGGGTGCCGTG TGGTGCATGT GGACTGTGGA ACACCAATG CCCTTCGTGCACACCAATGTTCCACAGTCCATGTTCAGCT FABP5 NM_001444  845 GCTGATGGCA  846 CTTTCCTTCC  847 CCTGATGCTGAA  848 GCTGATGGCAGAAAAACTCAGACTGTCTGCAACTTTACAGATG GAAAAACTCA CATCCCACT CCAATGCACCAT GTGCATTGGTTCAGCATCAGGAGTGGGATGGGAAGGAAAG FADD NM_003824  849 GTTTTCGCGA  850 CTCCGGTGCC  851 AACGCGCTCTTG  852 GTTTTCGCGAGATAACGGTCGAAAACGCGCTCTTGTCGATTTC GATAACGGTC TGATTCAC TCGATTTCCTGT CTGTAGTGAATCAGGCACCGGAG FAM107A NM_007177  853 AAGTCAGGGA  854 GCTGGCCCTA  855 AATTGCCACACT  856 AAGTCAGGGAAAACCTGCGGAGAATTGCCACACTGACCAGCG AAACCTGCG CAGCTCTCT GACCAGCGAAGA AAGAGAGAGAGCTGTAGGGCCAGC FAM13C NM_198215  857 ATCTTCAAAG  858 GCTGGATACC  859 TCCTGACTTTCT  860 ATCTTCAAAGCGGAGAGCGGGAGGAGCCACGGAGAAAGTCAG CGGAGAGCG ACATGCTCTG CCGTGGCTCCTC GAGACAGAGCATGTGGTATCCAGC FAM171B NM_177454  861 CCAGGAAGGA  862 GTGGTCTGCC  863 TGAAGATTTTGA  864 CCAGGAAGGAAAAGCACTGTTGAAGATTTTGAAGCTAATACAT AAAGCACTGT CCTTCTTTTA AGCTAATACATC CCCCCACTAAAAGAAGGGGCAGACCAC CCCCAC FAM49B NM_016623  865 AGATGCAGAA  866 GCTGGATTGC  867 TGGCCAGCTCCT  868 AGATGCAGAAGGCATCTTGGAGGACTTGCAGTCATACAGAGG GGCATCTTGG CTCTCGTATT CTGTATGACTGC AGCTGGCCACGAAATACGAGAGGCAATCCAGC FAM73A NM_198549  869 TGAGAAGGTG  870 GGCCATTAAA  871 AAGACCTCATGC  872 TGAGAAGGTGCGCTATTCAAGTACAGAGACTTTAGCTGAAGAC CGCTATTCAA AGCTCAGTGC AGTTACTCATTC CTCATGCAGTTACTCATTCGCCGCACTGAGCTTTTAATGGCC GCC FAP NM_004460  873 GTTGGCTCAC  874 GACAGGACCG  875 AGCCACTGCAAA  876 GTTGGCTCACGTGGGTTACTGATGAACGAGTATGTTTGCAGTG GTGGGTTAC AAACATTCTG CATACTCGTTCA GCTAAAAAGAGTCCAGAATGTTTCGGTCCTGTC TCA FAS NM_000043  877 GGATTGCTCA  878 GGCATTAACA  879 TCTGGACCCTCC  880 GGATTGCTCAACAACCATGCTGGGCATCTGGACCCTCCTACCT ACAACCATGC CTTTTGGACG TACCTCTGGTTC CTGGTTCTTACGTCTGTTGCTAGATTATCGTCCAAAAGTGTTA T ATAA TTACGT ATGCC FASLG NM_000639  881 GCACTTTGGG  882 GCATGTAAGA  883 ACAACATTCTCG  884 GCACTTTGGGATTCTTTCCATTATGATTCTTTGTTACAGGCAC ATTCTTTCCA AGACCCTCAC GTGCCTGTAACA CGAGAATGTTGTATTCAGTGAGGGTCTTCTTACATGC TTAT TGAA AAGAA FASN NM_004104  885 GCCTCTTCCT  886 GCTTTGCCCG  887 TCGCCCACCTAC  888 GCCTCTTCCTGTTCGACGGCTCGCCCACCTACGTACTGGCCTA GTTCGACG GTAGCTCT GTACTGGCCTAC CACCCAGAGCTACCGGGCAAAGC FCGR3A NM_000569  889 GTCTCCAGTG  890 AGGAATGCAG  891 CCCATGATCTTC  892 GTCTCCAGTGGAAGGGAAAAGCCCATGATCTTCAAGCAGGGA GAAGGGAAAA CTACTCACTG AAGCAGGGAAGC AGCCCCAGTGAGTAGCTGCATTCCT G FGF10 NM_004465  893 TCTTCCGTCC  894 AGAGTTGGTG  895 ACACCATGTCCT  896 TCTTCCGTCCCTGTCACCTGCCAAGCCCTTGGTCAGGACATGG CTGTCACCT GCCTCTGGT GACCAAGGGCTT TGTCACCAGAGGCCACCAACTCT FGF17 NM_003867  897 GGTGGCTGTC  898 TCTAGCCAGG  899 TTCTCGGATCTC  900 GGTGGCTGTCCTCAAAATCTGCTTCTCGGATCTCCCTCAGTCT CTCAAAATCT AGGAGTTTGG CCTCAGTCTGCC GCCCCCAGCCCCCAAACTCCTCCTGGCTAGA FGF5 NM_004464  901 GCATCGGTTT  902 AACATATTGG  903 CCATTGACTTTG  904 GCATCGGTTTCCATCTGCAGATCTACCCGGATGGCAAAGTCAA CCATCTGC CTTCGTGGGA CCATCCGGGTAG TGGATCCCACGAAGCCAATATGTT FGF6 NM_020996  905 GGGCCATTAA  906 CCCGGGACAT  907 CATCCACCTTGC  908 GGGCCATTAATTCTGACCACGTGCCTGAGAGGCAAGGTGGAT TTCTGACCAC AGTGATGAA CTCTCAGGCAC GGCCCTGGGACAGAAACTGTTCATCACTATGTCCCGGG FGF7 NM_002009  909 CCAGAGCAAA  910 TCCCCTCCTT  911 CAGCCCTGAGCG  912 CCAGAGCAAATGGCTACAAATGTGAACTGTTCCAGCCCTGAGC TGGCTACAAA CCATGTAATC ACACACAAGAAG GACACACAAGAAGTTATGATTACATGGAAGGAGGGGA FGFR2 NM_000141  913 GAGGGACTGT  914 GAGTGAGAAT  915 TCCCAGAGACCA  916 GAGGGACTGTTGGCATGCAGTGCCCTCCCAGAGACCAACGTT TGGCATGCA TCGATCCAAG ACGTTCAAGCAG CAAGCAGTTGGTAGAAGACTTGGATCGAATTCTCACTC TCTTC TTG FGFR4 NM_002011  917 CTGGCTTAAG  918 ACGAGACTCC  919 CCTTTCATGGGG  920 CTGGCTTAAGGATGGACAGGCCTTTCATGGGGAGAACCGCAT GATGGACAGG AGTGCTGATG AGAACCGCATT TGGAGGCATTCGGCTGCGCCATCAGCACTGGAGTCTCGT FKBP5 NM_004117  921 CCCACAGTAG  922 GGTTCTGGCT  923 TCTCCCCAGTTC  924 CCCACAGTAGAGGGGTCTCATGTCTCCCCAGTTCCACAGCAG AGGGGTCTCA TTCACGTCTG CACAGCAGTGTC TGTCACAGACGTGAAAGCCAGAACC FLNA NM_001456  925 GAACCTGCGG  926 GAAGACACCC  927 TACCAGGCCCAT  928 GAACCTGCGGTGGACACTTCCGGTGTCCAGTGCTATGGGCCT TGGACACT TGGCCCTC AGCACTGGACAC GGTATTGAGGGCCAGGGTGTCTTC FLNC NM_001458  929 CAGGACAATG  930 TGATGGTGTA  931 ATGTGCTGTCAG  932 CAGGACAATGGTGATGGCTCATGTGCTGTCAGCTACCTGCCCA GTGATGGCT CTCGCCAGG CTACCTGCCCAC CGGAGCCTGGCGAGTACACCATCA FLT1 NM_002019  933 GGCTCCTGAA  934 TCCCACAGCA  935 CTACAGCACCAA  936 GGCTCCTGAATCTATCTTTGACAAAATCTACAGCACCAAGAGC TCTATCTTTG ATACTCCGTA GAGCGACGTGTG GACGTGTGGTCTTACGGAGTATTGCTGTGGGA FLT4 NM_002020  937 ACCAAGAAGC  938 CCTGGAAGCT  939 AGCCCGCTGACC  940 ACCAAGAAGCTGAGGACCTGTGGCTGAGCCCGCTGACCATGG TGAGGACCTG GTAGCAGACA ATGGAAGATCT AAGATCTTGTCTGCTACAGCTTCCAGG FN1 NM_002026  941 GGAAGTGACA  942 ACACGGTAGC  943 ACTCTCAGGCGG  944 GGAAGTGACAGACGTGAAGGTCACCATCATGTGGACACCGCC GACGTGAAGG CGGTCACT TGTCCACATGAT TGAGAGTGCAGTGACCGGCTACCGTGT T FOS NM_005252  945 CGAGCCCTTT  946 GGAGCGGGCT  947 TCCCAGCATCAT  948 CGAGCCCTTTGATGACTTCCTGTTCCCAGCATCATCCAGGCCC GATGACTTCC GTCTCAGA CCAGGCCCAG AGTGGCTCTGAGACAGCCCGCTCC T FOXO1 NM_002015  949 GTAAGCACCA  950 GGGGCAGAGG  951 TATGAACCGCCT  952 GTAAGCACCATGCCCCACACCTCGGGTATGAACCGCCTGACC TGCCCCAC CACTTGTA GACCCAAGTGAA CAAGTGAAGACACCTGTACAAGTGCCTCTGCCCC FOXP3 NM_014009  953 CTGTTTGCTG  954 GTGGAGGAAC  955 TGTTTCCATGGC  956 CTGTTTGCTGTCCGGAGGCACCTGTGGGGTAGCCATGGAAAC TCCGGAGG TCTGGGAATG TACCCCACAGGT AGCACATTCCCAGAGTTCCTCCAC FOXQ1 NM_033260  957 TGTTTTTGTC  958 TGGAAAGGTT  959 TGATTTATGTCC  960 TGTTTTTGTCGCAACTTCCATTGATTTATGTCCCTTCCCTCCC GCAACTTCCA CCCTGATGTA CTTCCCTCCCCC CCCTAAGTACATCAGGGAACCTTTCCA CT FSD1 NM_024333  961 AGGCCTCCTG  962 TGTGTGAACC  963 CGCACCAAACAA  964 AGGCCTCCTGTCCTTCTACAATGCCCGCACCAAACAAGTGCTG TCCTTCTACA TGGTCTTGAA GTGCTGCACA CACACTTTCAAGACCAGGTTCACACA A FYN NM_002037  965 GAAGCGCAGA  966 CTCCTCAGAC  967 CTGAAGCACGAC  968 GAAGCGCAGATCATGAAGAAGCTGAAGCACGACAAGCTGGTC TCATGAAGAA ACCACTGCAT AAGCTGGTCCAG CAGCTCTATGCAGTGGTGTCTGAGGAG G6PD NM_000402  969 AATCTGCCTG  970 CGAGATGTTG  971 CCAGCCTCAGTG  972 AATCTGCCTGTGGCCTTGCCCGCCAGCCTCAGTGCCACTTGA TGGCCTTG CTGGTGACA CCACTTGACATT CATTCCTTGTCACCAGCAACATCTCG GABRG2 NM_198904  973 CCACTGTCCT  974 GAGATCCATC  975 CTCAGCACCATT  976 CCACTGTCCTGACAATGACCACCCTCAGCACCATTGCCCGGA GACAATGACC GCTGTGACAT GCCCGGAAAT AATCGCTCCCCAAGGTCTCCTATGTCACAGCGATGGATCTC GADD45A NM_001924  977 GTGCTGGTGA  978 CCCGGCAAAA  979 TTCATCTCAATG  980 GTGCTGGTGACGAATCCACATTCATCTCAATGGAAGGATCCTG CGAATCCA ACAAATAAGT GAAGGATCCTGC CCTTAAGTCAACTTATTTGTTTTTGCCGGG C GADD45B NM_015675  981 ACCCTCGACA  982 TGGGAGTTCA  983 TGGGAGTTCATG  984 ACCCTCGACAAGACCACACTTTGGGACTTGGGAGCTGGGGCT AGACCACACT TGGGTACAGA GGTACAGA GAAGTTGCTCTGTACCCATGAACTCCCA GDF15 NM_004864  985 CGCTCCAGAC  986 ACAGTGGAAG  987 TGTTAGCCAAAG  988 CGCTCCAGACCTATGATGACTTGTTAGCCAAAGACTGCCACTG CTATGATGAC GACCAGGACT ACTGCCACTGCA CATATGAGCAGTCCTGGTCCTTCCACTGT T GHR NM_000163  989 CCACCTCCCA  990 GGTGCGTGCC  991 CGTGCCTCAGCC  992 CCACCTCCCACAGGTTCAGGCGATTCCCGTGCCTCAGCCTCC CAGGTTCA TGTAGTCC TCCTGAGTAGCT TGAGTAGCTGGGACTACAGGCACGCACC GNPTAB NM_024312  993 GGATTCACAT  994 GTTCTTGCAT  995 CCCTGCTCACAT  996 GGATTCACATCGCGGAAAGTCCCTGCTCACATGCCTCACATGA CGCGGAAA AACAATCCGG GCCTCACATGAT TTGACCGGATTGTTATGCAAGAAC TC GNRH1 NM_000825  997 AAGGGCTAAA  998 CTGGATCTCT  999 TCCTGTCCTTCA 1000 AAGGGCTAAATCCAGGTGTGACGGTATCTAATGATGTCCTGTC TCCAGGTGTG GTGGCTGGT CTGTCCTTGCCA CTTCACTGTCCTTGCCATCACCAGCCACAGAGATCCAG GPM6B NM_ 1001 ATGTGCTTGG 1002 TGTAGAACAT 1003 CGCTGAGAAACC 1004 ATGTGCTTGGAGTGGCCTGGCTGGGTGTGTTTGGTTTCTCAGC 001001994 AGTGGCCT AAACACGGGC AAACACACCCAG GGTGCCCGTGTTTATGTTCTACA A GPNMB NM_ 1005 CAGCCTCGCC 1006 TGACAAATAT 1007 CAAACAGTGCCC 1008 CAGCCTCGCCTTTAAGGATGGCAAACAGTGCCCTGATCTCCGT 001005340 TTTTAAGGA GGCCAAGCAG TGATCTCCGTTG TGGCTGCTTGGCCATATTTGTCA GPR68 NM_003485 1009 CAAGGACCAG 1010 GGTAGGGCAG 1011 CTCAGCACCGTG 1012 CAAGGACCAGATCCAGCGGCTGGTGCTCAGCACCGTGGTCAT ATCCAGCG GAAGCAGG GTCATCTTCCTG CTTCCTGGCCTGCTTCCTGCCCTACC GPS1 NM_004127 1013 AGTACAAGCA 1014 GCAGCTCAGG 1015 CCTCCTGCTGGC 1016 AGTACAAGCAGGCTGCCAAGTGCCTCCTGCTGGCTTCCTTTGA GGCTGCCAAG GAAGTCACA TTCCTTTGATCA TCACTGTGACTTCCCTGAGCTGC GRB7 NM_005310 1017 CCATCTGCAT 1018 GGCCACCAGG 1019 CTCCCCACCCTT 1020 CCATCTGCATCCATCTTGTTTGGGCTCCCCACCCTTGAGAAGT CCATCTTGTT GTATTATCTG GAGAAGTGCCT GCCTCAGATAATACCCTGGTGGCC GREM1 NM_013372 1021 GTGTGGGCAA 1022 GACCTGATTT 1023 TCCACCCTCCCT 1024 GTGTGGGCAAGGACAAGCAGGATAGTGGAGTGAGAAAGGGAG GGACAAGC GGCCTCACC TTCTCACTCCAC GGTGGAGGGTGAGGCCAAATCAGGTC GSK3B NM_002093 1025 GACAAGGACG 1026 TTGTGGCCTG 1027 CCAGGAGTTGCC 1028 GACAAGGACGGCAGCAAGGTGACAACAGTGGTGGCAACTCCT GCAGCAAG TCTGGACC ACCACTGTTGTC GGGCAGGGTCCAGACAGGCCACAA GSN NM_000177 1029 CTTCTGCTAA 1030 GGCTCAAAGC 1031 ACCCAGCCAATC 1032 CTTCTGCTAAGCGGTACATCGAGACGGACCCAGCCAATCGGG GCGGTACATC CTTGCTTCAC GGGATCGGC ATCGGCGGACGCCCATCACCGTGGTGAAGCAAGGCTTTGAGC GA C GSTM1 NM_000561 1033 AAGCTATGAG 1034 GGCCCAGCTT 1035 TCAGCCACTGGC 1036 AAGCTATGAGGAAAAGAAGTACACGATGGGGGACGCTCCTGA GAAAAGAAGT GAATTTTTCA TTCTGTCATAAT TTATGACAGAAGCCAGTGGCTGAATGAAAAATTCAAGCTGGGC ACACGAT CAGGAG C GSTM2 NM_000848 1037 CTGCAGGCAC 1038 CCAAGAAACC 1039 CTGAAGCTCTAC 1040 CTGCAGGCACTCCCTGAAATGCTGAAGCTCTACTCACAGTTTC TCCCTGAAAT ATGGCTGCTT TCACAGTTTCTG TGGGGAAGCAGCCATGGTTTCTTGG GG HDAC1 NM_004964 1041 CAAGTACCAC 1042 GCTTGCTGTA 1043 TTCTTGCGCTCC 1044 CAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATC AGCGATGACT CTCCGACATG ATCCGTCCAGA CGTCCAGATAACATGTCGGAGTACAGCAAGC ACATTAA TT HDAC9 NM_178423 1045 AACCAGGCAG 1046 CTCTGTCTTC 1047 CCCCCTGAAGCT 1048 AACCAGGCAGTCACCTTGAGGAAGCAGAGGAAGAGCTTCAGG TCACCTTGAG CTGCATCGC CTTCCTCTGCTT GGGACCAGGCGATGCAGGAAGACAGAG HGD NM_000187 1049 CTCAGGTCTG 1050 TTATTGGTGC 1051 CTGAGCAGCTCT 1052 CTCAGGTCTGCCCCTACAATCTCTATGCTGAGCAGCTCTCAGG CCCCTACAAT TCCGTGGAC CAGGATCGGCTT ATCGGCTTTCACTTGTCCACGGAGCACCAATAA HIP1 NM_005338 1053 CTCAGAGCCC 1054 GGGTTTCCCT 1055 CGACTCACTGAC 1056 CTCAGAGCCCCACCTGAGCCTGCCGACTCACTGACCGAGGCC CACCTGAG GCCATACTG CGAGGCCTGTAA TGTAAGCAGTATGGCAGGGAAACCC HIRIP3 NM_003609 1057 GGATGAGGAA 1058 TCCCTAGCTG 1059 CCATTGCTCCTG 1060 GGATGAGGAAAAGGGGGATTGGAAACCCAGAACCAGGAGCAA AAGGGGGAT ACTTTCTCCG GTTCTGGGTTTC TGGCCGGAGAAAGTCAGCTAGGGA HK1 NM_000188 1061 TACGCACAGA 1062 GAGAGAAGTG 1063 TAAGAGTCCGGG 1064 TACGCACAGAGGCAAGCAGCTAAGAGTCCGGGATCCCCAGCC GGCAAGCA CTGGAGAGGC ATCCCCAGCCTA TACTGCCTCTCCAGCACTTCTCTC HLA-G NM_002127 1065 CCATCCCCAT 1066 CCGCAGCTCC 1067 CTGCAAGGACAA 1068 CCTGCGCGGCTACTACAACCAGAGCGAGGCCAGTTCTCACAC CATGGGTATC AGTGACTACA CCAGGCCAGCAA CCTCCAGTGGATGATTGGCTGCGACCTG HLF NM_002126 1069 CACCCTGCAG 1070 GGTACCTAGG 1071 TAAGTGATCTGC 1072 CACCCTGCAGGTGTCTGAGACTAAGTGATCTGCCCTCCAGGT GTGTCTGAG AGCAGAAGGT CCTCCAGGTGGC GGCGATCACCTTCTGCTCCTAGGTACC GA HNF1B NM_000458 1073 TCCCAGCATC 1074 CGTACCAGGT 1075 CCCCTATGAAGA 1076 TCCCAGCATCTCAACAAGGGCACCCCTATGAAGACCCAGAAG TCAACAAGG GTACAGAGCG CCCAGAAGCGTG CGTGCCGCTCTGTACACCTGGTACG HPS1 NM_000195 1077 GCGGAAGCTG 1078 TTCGGATAAG 1079 CAGTCACCAGCC 1080 GCGGAAGCTGTATGTGCTCAAGTACCTGTTTGAAGTGCACTTT TATGTGCTC ATGACCGTCC CAAAGTGCACTT GGGCTGGTGACTGTGGACGGTCATCTTATCCGAA HRAS NM_005343 1081 GGACGAATAC 1082 GCACGTCTCC 1083 ACCACCTGCTTC 1084 GGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCA GACCCCACT CCATCAAT CGGTAGGAATCC GGTGGTCATTGATGGGGAGACGTGC HSD17B10 NM_004493 1085 CCAGCGAGTT 1086 ATCTCACCAG 1087 TCATGGGCACCT 1088 CCACCAGACAAGACCGATTCGCTGGCCTCCATTTCTTCAACCC CTTGATGTGA CCACCAGG TCAATGTGATCC AGTGCCTGTCATGAAACTTGTGG HSD17B2 NM_002153 1089 GCTTTCCAAG 1090 TGCCTGCGAT 1091 AGTTGCTTCCAT 1092 GCTTTCCAAGTGGGGAATTAAAGTTGCTTCCATCCAACCTGGA TGGGGAATTA ATTTGTTAGG CCAACCTGGAGG GGCTTCCTAACAAATATCGCAGGCA HSD17B3 NM_000197 1093 GGGACGTCCT 1094 TGGAGAATCT 1095 CTTCATCCTCAC 1096 GGGACGTCCTGGAACAGTTCTTCATCCTCACAGGGCTGCTGG GGAACAGT CACGCACTTC AGGGCTGCTGGT TGTGCCTGGCCTGCCTGGCGAAGTGCGTGAGATTCTCCA HSD17B4 NM_000414 1097 CGGGAAGCTT 1098 ACCTCAGGCC 1099 AGGCGGCGTCCT 1100 CGGGAAGCTTCAGAGTACCTTTGTATTTGAGGAAATAGGACGC CAGAGTACCT CAATATCCTT ATTTCCTCAAAT CGCCTAAAGGATATTGGGCCTGAGGT T HSD3B2 NM_000198 1101 GCCTTCCTTT 1102 GGAGTAAATT 1103 ACTTCCAGCAGG 1104 GCCTTCCTTTAACCCTGATGTACTGGATTGGCTTCCTGCTGGA AACCCTGATG GGGCTGAGTA AAGCCAATCCAG AGTAGTGAGCTTCCTACTCAGCCCAATTTACTCC GG HSP90AB1 NM_007355 1105 GCATTGTGAC 1106 GAAGTGCCTG 1107 ATCCGCTCCATA 1108 GCATTGTGACCAGCACCTACGGCTGGACAGCCAATATGGAGC CAGCACCTAC GGCTTTCAT TTGGCTGTCCAG GGATCATGAAAGCCCAGGCACTTC HSPA5 NM_005347 1109 GGCTAGTAGA 1110 GGTCTGCCCA 1111 TAATTAGACCTA 1112 GGCTAGTAGAACTGGATCCCAACACCAAACTCTTAATTAGACC ACTGGATCCC AATGCTTTTC GGCCTCAGCTGC TAGGCCTCAGCTGCACTGCCCGAAAAGCATTTGGGCAGACC AACA ACTGCC HSPA8 NM_006597 1113 CCTCCCTCTG 1114 GCTACATCTA 1115 CTCAGGGCCCAC 1116 CCTCCCTCTGGTGGTGCTTCCTCAGGGCCCACCATTGAAGAG GTGGTGCTT CACTTGGTTG CATTGAAGAGGT GTTGATTAAGCCAACCAAGTGTAGATGTAGC GCTTAA TG HSPB1 NM_001540 1117 CCGACTGGAG 1118 ATGCTGGCTG 1119 CGCACTTTTCTG 1120 CCGACTGGAGGAGCATAAAAGCGCAGCCGAGCCCAGCGCCC GAGCATAAA ACTCTGCTC AGCAGACGTCCA CGCACTTTTCTGAGCAGACGTCCAGAGCAGAGTCAGCCAGCA T HSPB2 NM_001541 1121 CACCACTCCA 1122 TGGGACCAAA 1123 CACCTTTCCCTT 1124 CACCACTCCAGAGGTAGCAGCATCCTTGGGGGAAGGGAAAGG GAGGTAGCAG CCATACATTG CCCCCAAGGAT TGCATGGTCCACAATGTATGGTTTGGTCCCA HSPE1 NM_002157 1125 GCAAGCAACA 1126 CCAACTTTCA 1127 TCTCCACCCTTT 1128 GCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAGGAAA GTAGTCGCTG CGCTAACTGG CCTTTAGAACCC GGGTGGAGAGATTCAACCAGTTAGCGTGAAAGTTGG T G HSPG2 NM_005529 1129 GAGTACGTGT 1130 CTCAATGGTG 1131 CAGCTCCGTGCC 1132 GAGTACGTGTGCCGAGTGTTGGGCAGCTCCGTGCCTCTAGAG GCCGAGTGTT ACCAGGACA TCTAGAGGCCT GCCTCTGTCCTGGTCACCATTGAG ICAM1 NM_000201 1133 GCAGACAGTG 1134 CTTCTGAGAC 1135 CCGGCGCCCAAC 1136 GCAGACAGTGACCATCTACAGCTTTCCGGCGCCCAACGTGATT ACCATCTACA CTCTGGCTTC GTGATTCT CTGACGAAGCCAGAGGTCTCAGAAG GCTT GT IER3 NM_003897 1137 GTACCTGGTG 1138 GCGTCTCCGC 1139 TCAAGTTGCCTC 1140 GTACCTGGTGCGCGAGAGCGTATCCCCAACTGGGACTTCCGA CGCGAGAG TGTAGTGTT GGAAGTCCCAGT GGCAACTTGAACTCAGAACACTACAGCGGAGACGC IFI30 NM_006332 1141 ATCCCATGAA 1142 GCACCATTCT 1143 AAAATTCCACCC 1144 ATCCCATGAAGCCCAGATACACAAAATTCCACCCCATGATCAA GCCCAGATAC TAGTGGAGCA CATGATCAAGAA GAATCCTGCTCCACTAAGAATGGTGC TCC IFIT1 NM_001548 1145 TGACAACCAA 1146 CAGTCTGCCC 1147 AAGTTGCCCCAG 1148 TGACAACCAAGCAAATGTGAGGAGTCTGGTGACCTGGGGCAA GCAAATGTGA ATGTGGTAAT GTCACCAGACTC CTTTGCCTGGATGTATTACCACATGGGCAGACTG IFNG NM_000619 1149 GCTAAAACAG 1150 CAACCATTAC 1151 TCGACCTCGAAA 1152 GCTAAAACAGGGAAGCGAAAAAGGAGTCAGATGCTGTTTCGA GGAAGCGAAA TGGGATGCTC CAGCATCTGACT GGTCGAAGAGCATCCCAGTAATGGTTG CC IGF1 NM_000618 1153 TCCGGAGCTG 1154 CGGACAGAGC 1155 TGTATTGCGCAC 1156 TCCGGAGCTGTGATCTAAGGAGGCTGGAGATGTATTGCGCAC TGATCTAAGG GAGCTGACTT CCCTCAAGCCTG CCCTCAAGCCTGCCAAGTCAGCTCGCTCTGTCCG A IGF1R NM_000875 1157 GCATGGTAGC 1158 TTTCCGGTAA 1159 CGCGTCATACCA 1160 GCATGGTAGCCGAAGATTTCACAGTCAAAATCGGAGATTTTGG CGAAGATTTC TAGTCTGTCT AAATCTCCGATT TATGACGCGAGATATCTATGAGACAGACTATTACCGGAAA A CATAGATATC TTGA IGF2 NM_000612 1161 CCGTGCTTCC 1162 TGGACTGCTT 1163 TACCCCGTGGGC 1164 CCGTGCTTCCGGACAACTTCCCCAGATACCCCGTGGGCAAGT GGACAACTT CCAGGTGTCA AAGTTCTTCCAA TCTTCCAATATGACACCTGGAAGCAGTCCA IGFBP2 NM_000597 1165 GTGGACAGCA 1166 CCTTCATACC 1167 CTTCCGGCCAGC 1168 GTGGACAGCACCATGAACATGTTGGGCGGGGGAGGCAGTGCT CCATGAACA CGACTTGAGG ACTGCCTC GGCCGGAAGCCCCTCAAGTCGGGTATGAAGG IGFBP3 NM_000598 1169 ACATCCCAAC 1170 CCACGCCCTT 1171 ACACCACAGAAG 1172 ACATCCCAACGCATGCTCCTGGAGCTCACAGCCTTCTGTGGTG GCATGCTC GTTTCAGA GCTGTGAGCTCC TCATTTCTGAAACAAGGGCGTGG IGFBP5 NM_000599 1173 TGGACAAGTA 1174 CGAAGGTGTG 1175 CCCGTCAACGTA 1176 TGGACAAGTACGGGATGAAGCTGCCAGGCATGGAGTACGTTG CGGGATGAAG GCACTGAAAG CTCCATGCCTGG ACGGGGACTTTCAGTGCCACACCTTCG CT T IGFBP6 NM_002178 1177 TGAACCGCAG 1178 GTCTTGGACA 1179 ATCCAGGCACCT 1180 TGAACCGCAGAGACCAACAGAGGAATCCAGGCACCTCTACCA AGACCAACAG CCCGCAGAAT CTACCACGCCCT CGCCCTCCCAGCCCAATTCTGCGGGTGTCCAAGAC C IL10 NM_000572 1181 CTGACCACGC 1182 CCAAGCCCAG 1183 TTGAGCTGTTTT 1184 CTGACCACGCTTTCTAGCTGTTGAGCTGTTTTCCCTGACCTCC TTTCTAGCTG AGACAAGATA CCCTGACCTCCC CTCTAATTTATCTTGTCTCTGGGCTTGG A IL11 NM_000641 1185 TGGAAGGTTC 1186 TCTTGACCTT 1187 CCTGTGATCAAC 1188 TGGAAGGTTCCACAAGTCACCCTGTGATCAACAGTACCCGTAT CACAAGTCAC GCAGCTTTGT AGTACCCGTATG GGGACAAAGCTGCAAGGTCAAGA GG IL17A NM_002190 1189 TCAAGCAACA 1190 CAGCTCCTTT 1191 TGGCTTCTGTCT 1192 TCAAGCAACACTCCTAGGGCCTGGCTTCTGTCTGATCAAGGCA CTCCTAGGGC CTGGGTTGTG GATCAAGGCACC CCACACAACCCAGAAAGGAGCTG IL1A NM_000575 1193 GGTCCTTGGT 1194 GGATGGAGCT 1195 TCTCCACCCTGG 1196 GGTCCTTGGTAGAGGGCTACTTTACTGTAACAGGGCCAGGGT AGAGGGCTAC TCAGGAGAGA CCCTGTTACAGT GGAGAGTTCTCTCCTGAAGCTCCATCC TT IL1B NM_000576 1197 AGCTGAGGAA 1198 GGAAAGAAGG 1199 TGCCCACAGACC 1200 AGCTGAGGAAGATGCTGGTTCCCTGCCCACAGACCTTCCAGG GATGCTGGTT TGCTCAGGTC TTCCAGGAGAAT AGAATGACCTGAGCACCTTCTTTCC IL2 NM_000586 1201 ACCTCAACTC 1202 CACTGTTTGT 1203 TGCAACTCCTGT 1204 ACCTCAACTCCTGCCACAATGTACAGGATGCAACTCCTGTCTT CTGCCACAAT GACAAGTGCA CTTGCATTGCAC GCATTGCACTAAGTCTTGCACTTGTCACAAACAGTG AG IL6 NM_000600 1205 CCTGAACCTT 1206 ACCAGGCAAG 1207 CCAGATTGGAAG 1208 CCTGAACCTTCCAAAGATGGCTGAAAAAGATGGATGCTTCCAA CCAAAGATGG TCTCCTCATT CATCCATCTTTT TCTGGATTCAATGAGGAGACTTGCCTGGT TCA IL6R NM_000565 1209 CCAGCTTATC 1210 CTGGCGTAGA 1211 CCTTTGGCTTCA 1212 CCAGCTTATCTCAGGGGTGTGCGGCCTTTGGCTTCACGGAAG TCAGGGGTGT ACCTTCCG CGGAAGAGCCTT AGCCTTGCGGAAGGTTCTACGCCAG IL6ST NM_002184 1213 GGCCTAATGT 1214 AAAATTGTGC 1215 CATATTGCCCAG 1216 GGCCTAATGTTCCAGATCCTTCAAAGAGTCATATTGCCCAGTG TCCAGATCCT CTTGGAGGAG TGGTCACCTCAC GTCACCTCACACTCCTCCAAGGCACAATTTT A IL8 NM_000584 1217 AAGGAACCAT 1218 ATCAGGAAGG 1219 TGACTTCCAAGC 1220 AAGGAACCATCTCACTGTGTGTAAACATGACTTCCAAGCTGGC CTCACTGTGT CTGCCAAGAG TGGCCGTGGC CGTGGCTCTCTTGGCAGCCTTCCTGAT GTAAAC ILF3 NM_004516 1221 GACACGCCAA 1222 CTCAAGACCC 1223 ACACAAGACTTC 1224 GACACGCCAAGTGGTTCCAGGCCAGAGCCAACGGGCTGAAGT GTGGTTCC GGATCACAA AGCCCGTTGGCT CTTGTGTCATTGTGATCCGGGTCTTGAG ILK NM_ 1225 CTCAGGATTT 1226 AGGAGCAGGT 1227 ATGTGCTCCCAG 1228 CTCAGGATTTTCTCGCATCCAAATGTGCTCCCAGTGCTAGGTG 001014794 TCTCGCATCC GGAGACTGG TGCTAGGTGCCT CCTGCCAGTCTCCACCTGCTCCT IMMT NM_006839 1229 CTGCCTATGC 1230 GCTTTTCTGG 1231 CAACTGCATGGC 1232 CTGCCTATGCCAGACTCAGAGGAATCGAACAGGCTGTTCAGA CAGACTCAGA CTTCCTCTTC TCTGAACAGCCT GCCATGCAGTTGCTGAAGAGGAAGCCAGAAAAGC ING5 NM_032329 1233 CCTACAGCAA 1234 CATCTCGTAG 1235 CCAGCTGCACTT 1236 CCTACAGCAAGTGCAAGGAATACAGTGACGACAAAGTGCAGC GTGCAAGGAA GTCTGCATGG TGTCGTCACTGT TGGCCATGCAGACCTACGAGATG INHBA NM_002192 1237 GTGCCCGAGC 1238 CGGTAGTGGT 1239 ACGTCCGGGTCC 1240 GTGCCCGAGCCATATAGCAGGCACGTCCGGGTCCTCACTGTC CATATAGCA TGATGACTGT TCACTGTCCTTC CTTCCACTCAACAGTCATCAACCACTACCG TGA C INSL4 NM_002195 1241 CTGTCATATT 1242 CAGATTCCAG 1243 TGAGAAGACATT 1244 CTGTCATATTGCCCCATGCCTGAGAAGACATTCACCACCACCC GCCCCATGC CAGCCACC CACCACCACCCC CAGGAGGGTGGCTGCTGGAATCTG ITGA1 NM_181501 1245 GCTTCTTCTG 1246 CCTGTAGATA 1247 TTGCTGGACAGC 1248 GCTTCTTCTGGAGATGTGCTCTATATTGCTGGACAGCCTCGGT GAGATGTGCT ATGACCTGGC CTCGGTACAATC ACAATCATACAGGCCAGGTCATTATCTACAGG CT CT ITGA3 NM_002204 1249 CCATGATCCT 1250 GAAGCTTTGT 1251 CACTCCAGACCT 1252 CCATGATCCTCACTCTGCTGGTGGACTATACACTCCAGACCTC CACTCTGCTG AGCCGGTGAT CGCTTAGCATGG GCTTAGCATGGTAAATCACCGGCTACAAAGCTTC ITGA4 NM_000885 1253 CAACGCTTCA 1254 GTCTGGCCGG 1255 CGATCCTGCATC 1256 CAACGCTTCAGTGATCAATCCCGGGGCGATTTACAGATGCAG GTGATCAATC GATTCTTT TGTAAATCGCCC GATCGGAAAGAATCCCGGCCAGAC C ITGA5 NM_002205 1257 AGGCCAGCCC 1258 GTCTTCTCCA 1259 TCTGAGCCTTGT 1260 AGGCCAGCCCTACATTATCAGAGCAAGAGCCGGATAGAGGAC TACATTATCA CAGTCCAGCA CCTCTATCCGGC AAGGCTCAGATCTTGCTGGACTGTGGAGAAGAC ITGA6 NM_000210 1261 CAGTGACAAA 1262 GTTTAGCCTC 1263 TCGCCATCTTTT 1264 CAGTGACAAACAGCCCTTCCAACCCAAGGAATCCCACAAAAGA CAGCCCTTCC ATGGGCGTC GTGGGATTCCTT TGGCGATGACGCCCATGAGGCTAAAC ITGA7 NM_002206 1265 GATATGATTG 1266 AGAACTTCCA 1267 CAGCCAGGACCT 1268 GATATGATTGGTCGCTGCTTTGTGCTCAGCCAGGACCTGGCCA GTCGCTGCTT TTCCCCACCA GGCCATCCG TCCGGGATGAGTTGGATGGTGGGGAATGGAAGTTCT TG T ITGAD NM_005353 1269 GAGCCTGGTG 1270 ACTGTCAGGA 1271 CAACTGAAAGGC 1272 GAGCCTGGTGGATCCCATCGTCCAACTGAAAGGCCTGACGTT GATCCCAT TGCCCGTG CTGACGTTCACG CACGGCCACGGGCATCCTGACAGT ITGB3 NM_000212 1273 ACCGGGAGCC 1274 CCTTAAGCTC 1275 AAATACCTGCAA 1276 ACCGGGGAGCCCTACATGACGAAAATACCTGCAACCGTTACT CTACATGAC TTTCACTGAC CCGTTACTGCCG GCCGTGACGAGATTGAGTCAGTGAAAGAGCTTAAGG TCAATCT TGAC ITGB4 NM_000213 1277 CAAGGTGCCC 1278 GCGCACACCT 1279 CACCAACCTGTA 1280 CAAGGTGCCCTCAGTGGAGCTCACCAACCTGTACCCGTATTG TCAGTGGA TCATCTCAT CCCGTATTGCGA CGACTATGAGATGAAGGTGTGCGC ITGB5 NM_002213 1281 TCGTGAAAGA 1282 GGTGAACATC 1283 TGCTATGTTTCT 1284 TCGTGAAAGATGACCAGGAGGCTGTGCTATGTTTCTACAAAAC TGACCAGGAG ATGACGCAGT ACAAAACCGCCA CGCCAAGGACTGCGTCATGATGTTCACC AGG ITPR1 NM_002222 1285 GAGGAGGTGT 1286 GTAATCCCAT 1287 CCATCCTAACGG 1288 GAGGAGGTGTGGGTGTTCCGCTTCCATCCTAACGGAACGAGC GGGTGTTCC GTCCGCGA AACGAGCTCCCT TCCCTCTTCGCGGACATGGGATTAC ITPR3 NM_002224 1289 TTGCCATCGT 1290 ATGGAGCTGG 1291 TCCAGGTCTCGG 1292 TTGCCATCGTGTCAGTGCCCGTGTCTGAGATCCGAGACCTGG GTCAGTGC CGTCATTG ATCTCAGACACG ACTTTGCCAATGACGCCAGCTCCAT ITSN1 NM_003024 1293 TAACTGGGAT 1294 CTCTGCCTTA 1295 AGCCCTCTCTCA 1296 TAACTGGGATGCATGGGCAGCCCAGCCCTCTCTCACCGTTCC GCATGGGC ACTGGCCG CCGTTCCAAGTG AAGTGCCGGCCAGTTAAGGCAGAG JAG1 NM_000214 1297 TGGCTTACAC 1298 GCATAGCTGT 1299 ACTCGATTTCCC 1300 TGGCTTACACTGGCAATGGTAGTTTCTGTGGTTGGCTGGGAAA TGGCAATGG GAGATGCGG AGCCAACCACAG TCGAGTGCCGCATCTCACAGCTATGC JUN NM_002228 1301 GACTGCAAAG 1302 TAGCCATAAG 1303 CTATGACGATGC 1304 GACTGCAAAGATGGAAACGACCTTCTATGACGATGCCCTCAAC ATGGAAACGA GTCCGCTCTC CCTCAACGCCTC GCCTCGTTCCTCCCGTCCGAGAGCGGACCTTATGGCTA JUNB NM_002229 1305 CTGTCAGCTG 1306 AGGGGGTGTC 1307 CAAGGGACACGC 1308 CTGTCAGCTGCTGCTTGGGGTCAAGGGACACGCCTTCTGAAC CTGCTTGG CGTAAAGG CTTCTGAACGT GTCCCCTGCCCCTTTACGGACACCCCCT KCNN2 NM_021614 1309 TGTGCTATTC 1310 GGGCATAGGA 1311 TTATACATTCAC 1312 TGTGCTATTCATCCCATACCTGGGAATTATACATTCACATGGA ATCCCATACC GAAGGCAAG ATGGACGGCCCG CGGCCCGGCTTGCCTTCTCCTATGCCC TG KCTD12 NM_138444 1313 AGCAGTTACT 1314 TGGAGACCTG 1315 ACTCTTAGGCGG 1316 AGCAGTTACTGGCAAGAGGGAGAAAGGACGCTGCCGCCTAAG GGCAAGAGGG AGCAGCCT CAGCGTCCTTTC AGTGCAAGGCTGCTCAGGTCTCCA KHDRBS3 NM_006558 1317 CGGGCAAGAA 1318 CTGTAGACGC 1319 CAAGACACAAGG 1320 CGGGCAAGAAGAGTGGACTAACTCAAGACACAAGGCACCTTC GAGTGGAC CCTTTGCTGT CACCTTCAGCGA AGCGAGGACAGCAAAGGGCGTCTACAG KIAA0196 NM_014846 1321 CAGACACCAG 1322 AACATTGTGA 1323 TCCCCAGTGTCC 1324 CAGACACCAGCTCTGAGGCCAGTTAATCATCCCCAGTGTCCAG CTCTGAGGC GGCGGACC AGGCACAGAGTA GCACAGAGTAGTCGGTCCGCCTCACAATGTT KIAA0247 NM_014734 1325 CCGTGGGACA 1326 GAAGCAAGTC 1327 TCCGCTAGTGAT 1328 CCGTGGGACATGGAGTGTTCCTTCCGCTAGTGATCCTTTGCAC TGGAGTGT CGTCTCCAAG CCTTTGCACCCT CCTGCTTGGAGACGGACTTGCTTC KIF4A NM_012310 1329 AGAGCTGGTC 1330 GCTGGTCTTG 1331 CAGGTCAGCAAA 1332 AGAGCTGGTCTCCTCCAAAATACAGGTCAGCAAACTTGAAAGC TCCTCCAAAA CTCTGTTTCA CTTGAAAGCAGC AGCCTGAAACAGAGCAAGACCAGC C KIT NM_000222 1333 GAGGCAACTG 1334 GGCACTCGGC 1335 TTACAGCGACAG 1336 GAGGCAACTGCTTATGGCTTAATTAAGTCAGATGCGGCCATGA CTTATGGCTT TTGAGCAT TCATGGCCGCAT CTGTCGCTGTAAAGATGCTCAAGCCGAGTGCC AATTA KLC1 NM_182923 1337 AGTGGCTACG 1338 TGAGCCACAG 1339 CAACACGCAGCA 1340 AGTGGCTACGGGATGAACTGGCCAACACGCAGCAGAAACTGC GGATGAACTG ACTGCTCACT GAAACTGCAGAA AGAAGAGTGAGCAGTCTGTGGCTCA KLF6 NM_001300 1341 CACGAGACCG 1342 GCTCTAGGCA 1343 AGTACTCCTCCA 1344 CACGAGACCGGCTACTTCTCGGCGCTGCCGTCTCTGGAGGAG GCTACTTCTC GGTCTGTTGC GAGACGGCAGCG TACTGGCAACAGACCTGCCTAGAGC KLK1 NM_002257 1345 AACACAGCCC 1346 CCAGGAGGCT 1347 TCAGTGAGAGCT 1348 AACACAGCCCAGTTTGTTCATGTCAGTGAGAGCTTCCCACACC AGTTTGTTCA CATGTTGAAG TCCCACACCCTG CTGGCTTCAACATGAGCCTCCTGG KLK10 NM_002776 1349 GCCCAGAGGC 1350 CAGAGGTTTG 1351 CCTCTTCCTCCC 1352 GCCCAGAGGCTCCATCGTCCATCCTCTTCCTCCCCAGTCGGCT TCCATCGT AACAGTGCAG CAGTCGGCTGA GAACTCTCCCCTTGTCTGCACTGTTCAAACCTCTG ACA KLK11 NM_006853 1353 CACCCCGGCT 1354 CATCTTCACC 1355 CCTCCCCAACAA 1356 CACCCCGGCTTCAACAACAGCCTCCCCAACAAAGACCACCGC TCAACAAC AGCATGATGT AGACCACCGCA AATGACATCATGCTGGTGAAGATG CA KLK14 NM_022046 1357 CCCCTAAAAT 1358 CTCATCCTCT 1359 CAGCACTTCAAG 1360 CCCCTAAAATGTTCCTCCTGCTGACAGCACTTCAAGTCCTGGC GTTCCTCCTG TGGCTCTGTG TCCTGGCTATAG TATAGCCATGACACAGAGCCAAGAGGATGAG CCA KLK2 NM_005551 1361 AGTCTCGGAT 1362 TGTACACAGC 1363 TTGGGAATGCTT 1364 AGTCTCGGATTGTGGGAGGCTGGGAGTGTGAGAAGCATTCCC TGTGGGAGG CACCTGCC CTCACACTCCCA AACCCTGGCAGGTGGCTGTGTACA KLK3 NM_001648 1365 CCAAGCTTAC 1366 AGGGTGAGGA 1367 ACCCACATGGTG 1368 CCAAGCTTACCACCTGCACCCGGAGAGCTGTGTCACCATGTG CACCTGCAC AGACAACCG ACACAGCTCTCC GGTCCCGGTTGTCTTCCTCACCCT KLRK1 NM_007360 1369 TGAGAGCCAG 1370 ATCCTGGTCC 1371 TGTCTCAAAATG 1372 TGAGAGCCAGGCTTCTTGTATGTCTCAAAATGCCAGCCTTCTG GCTTCTTGTA TCTTTGCTGT CCAGCCTTCTGA AAAGTATACAGCAAAGAGGACCAGGAT A KPNA2 NM_002266 1373 TGATGGTCCA 1374 AAGCTTCACA 1375 ACTCCTGTTTTC 1376 TGATGGTCCAAATGAACGAATTGGCATGGTGGTGAAAACAGGA AATGAACGAA AGTTGGGGC ACCACCATGCCA GTTGTGCCCCAACTTGTGAAGCTT KRT1 NM_006121 1377 TGGACAACAA 1378 TATCCTCGTA 1379 CCTCAGCAATGA 1380 TGGACAACAACCGCAGTCTCGACCTGGACAGCATCATTGCTGA CCGCAGTC CTGGGCCTTG TGCTGTCCAGGT GGTCAAGGCCCAGTACGAGGATA KRT15 NM_002275 1381 GCCTGGTTCT 1382 CTTGCTGGTC 1383 TGAACAAAGAGG 1384 GCCTGGTTCTTCAGCAAGACTGAGGAGCTGAACAAAGAGGTG TCAGCAAGAC TGGATCATTT TGGCCTCCAACA GCCTCCAACACAGAAATGATCCAGACCAGCAAG C KRT18 NM_000224 1385 AGAGATCGAG 1386 GGCCTTTTAC 1387 TGGTTCTTCTTC 1388 AGAGATCGAGGCTCTCAAGGAGGAGCTGCTCTTCATGAAGAA GCTCTCAAGG TTCCTCTTCG ATGAAGAGCAGC GAACCACGAAGAGGAAGTAAAAGGCC TCC KRT2 NM_000423 1389 CCAGTGACGC 1390 GGGCATGGCT 1391 ACCTAGACAGCA 1392 CCAGTGACGCCTCTGTGTTCTGGGGCGGAATCTGTGCTGTCTA CTCTGTGTT AGAAGCAC CAGATTCCGCCC GGTTTGTGCTTCTAGCCATGCCC KRT5 NM_000424 1393 TCAGTGGAGA 1394 TGCCATATCC 1395 CCAGTCAACATC 1396 TCAGTGGAGAAGGAGTTGGACCAGTCAACATCTCTGTTGTCAC AGGAGTTGGA AGAGGAAACA TCTGTTGTCACA AAGCAGTGTTTCCTCTGGATATGGCA AGCA KRT75 NM_004693 1397 TCAAAGTCAG 1398 ACGTCCTTTT 1399 TTCATTCTCAGC 1400 TCAAAGTCAGGTACGAAGATGAAATTAACAAGCGCACAGCTGC GTACGAAGAT TCAGGGCTAC AGCTGTGCGCTT TGAGAATGAATTTGTAGCCCTGAAAAAGGACGT GAAATT AA GT KRT76 NM_015848 1401 ATCTCCAGAC 1402 TCAGGGAATT 1403 TCTGGGCTTCAG 1404 ATCTCCAGACTGCTGGTTCCCAGGGAACCCTCCCTACATCTGG TGCTGGTTCC AGGGGACAGA ATCCTGACTCCC GCTTCAGATCCTGACTCCCTTCTGTCCCCTAATTCCCTGA KRT8 NM_002273 1405 GGATGAAGCT 1406 CATATAGCTG 1407 CGTCGGTCAGCC 1408 GGATGAAGCTTACATGAACAAGGTAGAGCTGGAGTCTCGCCT TACATGAACA CCTGAGGAAG CTTCCAGGC GGAAGGGCTGACCGACGAGATCAACTTCCTCAGGCAGCTATA AGGTAGA TTGAT TG L1CAM NM_000425 1409 CTTGCTGGCC 1410 TGATTGTCCG 1411 ATCTACGTTGTC 1412 CTTGCTGGCCAATGCCTACATCTACGTTGTCCAGCTGCCAGCC AATGCCTA CAGTCAGG CAGCTGCCAGCC AAGATCCTGACTGCGGACAATCA LAG3 NM_002286 1413 GCCTTAGAGC 1414 CGGTTCTTGC 1415 TCTATCTTGCTC 1416 GCCTTAGAGCAAGGGATTCACCCTCCGCAGGCTCAGAGCAAG AAGGGATTCA TCCAGCTC TGAGCCTGCGGA ATAGAGGAGCTGGAGCAAGAACCG LAMA3 NM_000227 1417 CCTGTCACTG 1418 TGGGTTACTG 1419 ATTCAGACTGAC 1420 CCTGTCACTGAAGCCTTGGAAGTCCAGGGGCCTGTCAGTCTG AAGCCTTGG GTCAGGACAA AGGCCCCTGGAC AATGGTTGTCCTGACCAGTAACCCA C LAMA4 NM_002290 1421 GATGCACTGC 1422 CAGAGGATAC 1423 CTCTCCATCGAG 1424 GATGCACTGCGGTTAGCAGCGCTCTCCATCGAGGAAGGCAAA GGTTAGCAG GCTCAGCACC GAAGGCAAATCC TCCGGGGTGCTGAGCGTATCCTCTG LAMA5 NM_005560 1425 CTCCTGGCCA 1426 ACACAAGGCC 1427 CTGTTCCTGGAG 1428 CTCCTGGCCAACAGCACTGCACTAGAAGAGGCCATGCTCCAG ACAGCACT CAGCCTCT CATGGCCTCTTC GAACAGCAGAGGCTGGGCCTTGTGT LAMB1 NM_002291 1429 CAAGGAGACT 1430 CGGCAGAACT 1431 CAAGTGCCTGTA 1432 CAAGGAGACTGGGAGGTGTCTCAAGTGCCTGTACCACACGGA GGGAGGTGTC GACAGTGTTC CCACACGGAAGG AGGGGAACACTGTCAGTTCTGCCG LAMB3 NM_000228 1433 ACTGACCAAG 1434 GTCACACTTG 1435 CCACTCGCCATA 1436 ACTGACCAAGCCTGAGACCTACTGCACCCAGTATGGCGAGTG CCTGAGACCT CAGCATTTCA CTGGGTGCAGT GCAGATGAAATGCTGCAAGTGTGAC LAMC1 NM_002293 1437 GCCGTGATCT 1438 ACCTGCTTGC 1439 CCTCGGTACTTC 1440 GCCGTGATCTCAGACAGCTACTTTCCTCGGTACTTCATTGCTC CAGACAGCTA CCAAGAACT ATTGCTCCTGCA CTGCAAAGTTCTTGGGCAAGCAGGT C LAMC2 NM_005562 1441 ACTCAAGCGG 1442 ACTCCCTGAA 1443 AGGTCTTATCAG 1444 ACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCACAGTC AAATTGAAGC GCCGAGACAC CACAGTCTCCGC TCCGCCTCCTGGATTCAGTGTCTCGGCTTCAGGGAGT A T CTCC LAPTM5 NM_006762 1445 TGCTGGACTT 1446 TGAGATAGGT 1447 TCCTGACCCTCT 1448 TGCTGGACTTCTGCCTGAGCATCCTGACCCTCTGCAGCTCCTA CTGCCTGAG GGGCACTTCC GCAGCTCCTACA CATGGAAGTGCCCACCTATCTCA LGALS3 NM_002306 1449 AGCGGAAAAT 1450 CTTGAGGGTT 1451 ACCCAGATAACG 1452 AGCGGAAAATGGCAGACAATTTTTCGCTCCATGATGCGTTATC GGCAGACAAT TGGGTTTCCA CATCATGGAGCG TGGGTCTGGAAACCCAAACCCTCAAG A LIG3 NM_002311 1453 GGAGGTGGAG 1454 ACAGGTGTCA 1455 CTGGACGCTCAG 1456 GGAGGTGGAGAAGGAGCCGGGCCAGAGACGAGCTCTGAGCG AAGGAGCC TCAGCGAGG AGCTCGTCTCTG TCCAGGCCTCGCTGATGACACCTGT LIMS1 NM_004987 1457 TGAACAGTAA 1458 TTCTGGGAAC 1459 ACTGAGCGCACA 1460 TGAACAGTAATGGGGAGCTGTACCATGAGCAGTGTTTCGTGTG TGGGGAGCTG TGCTGGAAG CGAAACACTGCT CGCTCAGTGCTTCCAGCAGTTCCCAGAA LOX NM_002317 1461 CCAATGGGAG 1462 CGCTGAGGCT 1463 CAGGCTCAGCAA 1464 CCAATGGGAGAACAACGGGCAGGTGTTCAGCTTGCTGAGCCT AACAACGG GGTACTGTG GCTGAACACCTG GGGCTCACAGTACCAGCCTCAGCG LRP1 NM_002332 1465 TTTGGCCCAA 1466 GTCTCGATGC 1467 TCCCGGCTGGGC 1468 TTTGGCCCAATGGGCTAAGCCTGGACATCCCGGCTGGGCGCC TGGGCTAAG GGTCGTAGAA GCCTCTACT TCTACTGGGTGGATGCCTTCTACGACCGCATCGAGAC G LTBP2 NM_000428 1469 GCACACCCAT 1470 GATGGCTGGC 1471 CTTTGCAGCCCT 1472 GCACACCCATCCTTGAGTCTCCTTTGCAGCCCTCAGAACTCCA CCTTGAGTCT CACGTAGT CAGAACTCCAGC GCCCCACTACGTGGCCAGCCATC LUM NM_002345 1473 GGCTCTTTTG 1474 AAAAGCAGCT 1475 CCTGACCTTCAT 1476 GGCTCTTTTGAAGGATTGGTAAACCTGACCTTCATCCATCTCC AAGGATTGGT GAAACAGCAT CCATCTCCAGCA AGCACAATCGGCTGAAAGAGGATGCTGTTTCAGCTGCTTTT AA C MAGEA4 NM_002362 1477 GCATCTAACA 1478 CAGAGTGAAG 1479 CAGCTTCCCTTG 1480 GCATCTAACAGCCCTGTGCAGCAGCTTCCCTTGCCTCGTGTAA GCCCTGTGC AATGGGCCTC CCTCGTGTAACA CATGAGGCCCATTCTTCACTCTG MANF NM_006010 1481 CAGATGTGAA 1482 AAGGGAATCC 1483 TTCCTGATGATG 1484 CAGATGTGAAGCCTGGAGCTTTCCTGATGATGCTGGCCCTACA GCCTGGAGC CCTCATGG CTGGCCCTACAG GTACCCCCATGAGGGGATTCCCTT MAOA NM_000240 1485 GTGTCAGCCA 1486 CGACTACGTC 1487 CCGCGATACTCG 1488 GTGTCAGCCAAAGCATGGAGAATCAAGAGAAGGCGAGTATCG AAGCATGGA GAACATGTGG CCTTCTCTTGAT CGGGCCACATGTTCGACGTAGTCG MAP3K5 NM_005923 1489 AGGACCAAGA 1490 CCTGTGGCCA 1491 CAGCCCAGAGAC 1492 AGGACCAAGAGGCTACGGAAAAGCAGCAGACATCTGGTCTCT GGCTACGGA TTTCAATGAT CAGATGTCTGCT GGGCTGTACAATCATTGAAATGGCCACAGG MAP3K7 NM_145333 1493 CAGGCAAGAA 1494 CCTGTACCAG 1495 TGCTGGTCCTTT 1496 CAGGCAAGAACTAGTTGCAGAACTGGACCAGGATGAAAAGGA CTAGTTGCAG GCGAGATGTA TCATCCTGGTCC CCAGCAAAATACATCTCGCCTGGTACAGG AA T MAP4K4 NM_004834 1497 TCGCCGAGAT 1498 CTGTTGTCTC 1499 AACGTTCCTTGT 1500 TCGCCGAGATTTCCTGAGACTGCAGCAGGAGAACAAGGAACG TTCCTGAG CGAAGAGCCT TCTCCTGCTGCA TTCCGAGGCTCTTCGGAGACAACAG MAP7 NM_003980 1501 GAGGAACAGA 1502 CTGCCAACTG 1503 CATGTACAACAA 1504 GAGGAACAGAGGTGTCTGCACTTCCATGTACAACAAACGCTCC GGTGTCTGCA GCTTTCCA ACGCTCCGGGAA GGGAAATGGAAAGCCAGTTGGCAG C MAPKAPK3 NM_004635 1505 AAGCTGCAGA 1506 GTGGGCAATG 1507 ATTGGCACTGCC 1508 AAGCTGCAGAGATAATGCGGGATATTGGCACTGCCATCCAGTT GATAATGCGG TTATGGCTG ATCCAGTTTCTG TCTGCACAGCCATAACATTGCCCAC MCM2 NM_004526 1509 GACTTTTGCC 1510 GCCACTAACT 1511 ACAGCTCATTGT 1512 GACTTTTGCCCGCTACCTTTCATTCCGGCGTGACAACAATGAG CGCTACCTTT GCTTCAGTAT TGTCACGCCGGA CTGTTGCTCTTCATACTGAAGCAGTTAGTGGC C GAAGAG MCM3 NM_002388 1513 GGAGAACAAT 1514 ATCTCCTGGA 1515 TGGCCTTTCTGT 1516 GGAGAACAATCCCCTTGAGACAGAATATGGCCTTTCTGTCTAC CCCCTTGAGA TGGTGATGGT CTACAAGGATCA AAGGATCACCAGACCATCACCATCCAGGAGAT CCA MCM6 NM_005915 1517 TGATGGTCCT 1518 TGGGACAGGA 1519 CAGGTTTCATAC 1520 TGATGGTCCTATGTGTCACATTCATCACAGGTTTCATACCAAC ATGTGTCACA AACACACCAA CAACACAGGCTT ACAGGCTTCAGCACTTCCTTTGGTGTGTTTCCTGTCCCA TTCA CAGCAC MDK NM_002391 1521 GGAGCCGACT 1522 GACTTTGGTG 1523 ATCACACGCACC 1524 GGAGCCGACTGCAAGTACAAGTTTGAGAACTGGGGTGCGTGT GCAAGTACA CCTGTGCC CCAGTTCTCAAA GATGGGGGCACAGGCACCAAAGTC MDM2 NM_002392 1525 CTACAGGGAC 1526 ATCCAACCAA 1527 CTTACACCAGCA 1528 CTACAGGGACGCCATCGAATCCGGATCTTGATGCTGGTGTAAG GCCATCGAA TCACCTGAAT TCAAGATCCGG TGAACATTCAGGTGATTGGTTGGAT GTT MELK NM_014791 1529 AGGATCGCCT 1530 TGCACATAAG 1531 CCCGGGTTGTCT 1532 AGGATCGCCTGTCAGAAGAGGAGACCCGGGTTGTCTTCCGTC GTCAGAAGAG CAACAGCAGA TCCGTCAGATAG AGATAGTATCTGCTGTTGCTTATGTGCA MET NM_000245 1533 GACATTTCCA 1534 CTCCGATCGC 1535 TGCCTCTCTGCC 1536 GACATTTCCAGTCCTGCAGTCAATGCCTCTCTGCCCCACCCTT GTCCTGCAGT ACACATTTGT CCACCCTTTGT TGTTCAGTGTGGCTGGTGCCACGACAAATGTGTGCGATCGGA CA G MGMT NM_002412 1537 GTGAAATGAA 1538 GACCCTGCTC 1539 CAGCCCTTTGGG 1540 GTGAAATGAAACGCACCACACTGGACAGCCCTTTGGGGAAGC ACGCACCACA ACAACCAGAC GAAGCTGG TGGAGCTGTCTGGTTGTGAGCAGGGTC MGST1 NM_020300 1541 ACGGATCTAC 1542 TCCATATCCA 1543 TTTGACACCCCT 1544 ACGGATCTACCACACCATTGCATATTTGACACCCCTTCCCCAG CACACCATTG ACAAAAAAAC TCCCCAGCCA CCAAATAGAGCTTTGAGTTTTTTTGTTGGATATGGA C TCAAAG MICA NM_000247 1545 ATGGTGAATG 1546 AAGCCAGAAG 1547 CGAGGCCTCAGA 1548 ATGGTGAATGTCACCCGCAGCGAGGCCTCAGAGGGCAACATT TCACCCGC CCCTGCAT GGGCAACATTAC ACCGTGACATGCAGGGCTTCTGGCTT MKI67 NM_002417 1549 GATTGCACCA 1550 TCCAAAGTGC 1551 CCACTCTTCCTT 1552 GATTGCACCAGGGCAGAACAGGGGAGGGTGTTCAAGGAAGAG GGGCAGAA CTCTGCTAAG GAACACCCTCCC TGGCTCTTAGCAGAGGCACTTTGGA A MLXIP NM_014938 1553 TGCTTAGCTG 1554 CAGCCTACTC 1555 CATGAGATGCCA 1556 TGCTTAGCTGGCATGTGGCCGCATGAGATGCCAGGAGACCCT GCATGTGG TCCATGGGC GGAGACCCTTCC TCCCTGCCCATGGAGAGTAGGCTG MMP11 NM_005940 1557 CCTGGAGGCT 1558 TACAATGGCT 1559 ATCCTCCTGAAG 1560 CCTGGAGGCTGCAACATACCTCAATCCTGTCCCAGGCCGGAT GCAACATACC TTGGAGGATA CCCTTTTCGCAG CCTCCTGAAGCCCTTTTCGCAGCACTGCTATCCTCCAAAGCCA GCA C TTGTA MMP2 NM_004530 1561 CAGCCAGAAG 1562 AGACACCATC 1563 AAGTCCGAATCT 1564 CAGCCAGAAGCGGAAACTTAAAAAGTCCGAATCTCTGCTCCCT CGGAAACTTA ACCTGTGCC CTGCTCCCTGCA GCAGGGCACAGGTGATGGTGTCT MMP7 NM_002423 1565 GGATGGTAGC 1566 GGAATGTCCC 1567 CCTGTATGCTGC 1568 GGATGGTAGCAGTCTAGGGATTAACTTCCTGTATGCTGCAACT AGTCTAGGGA ATACCCAAAG AACTCATGAACT CATGAACTTGGCCATTCTTTGGGTATGGGACATTCC TTAACT AA TGGC MMP9 NM_004994 1569 GAGAACCAAT 1570 CACCCGAGTG 1571 ACAGGTATTCCT 1572 GAGAACCAATCTCACCGACAGGCAGCTGGCAGAGGAATACCT CTCACCGACA TAACCATAGC CTGCCAGCTGCC GTACCGCTATGGTTACACTCGGGTG MPPED2 NM_001584 1573 CCGACCAACC 1574 AGGGCATTTA 1575 ATTTGACCTTCC 1576 CCGACCAACCCTCCAATTATATTTGACCTTCCAAACCCACAGG CTCCAATTA GAGCTTCAGG AAACCCACAGGG GTTCCTGAAGCTCTAAATGCCCT A MRC1 NM_002438 1577 CTTGACCTCA 1578 GGACTGCGGT 1579 CCAACCGCTGTT 1580 CTTGACCTCAGGACTCTGGATTGGACTTAACAGTCTGAGCTTC GGACTCTGGA CACTCCAC GAAGCTCAGACT AACAGCGGTTGGCAGTGGAGTGACCGCAGTCC TT MRPL13 NM_014078 1581 TCCGGTTCCC 1582 GTGGAAAAAC 1583 CGGCTGGAAATT 1584 TCCGGTTCCCTTCGTTTAGGTCGGCTGGAAATTATGTCCTCCG TTCGTTTAG TGCGGAAAAC ATGTCCTCCGTC TCGGTTTTCCGCAGTTTTTCCAC MSH2 NM_000251 1585 GATGCAGAAT 1586 TCTTGGCAAG 1587 CAAGAAGATTTA 1588 GATGCAGAATTGAGGCAGACTTTACAAGAAGATTTACTTCGTC TGAGGCAGAC TCGGTTAAGA CTTCGTCGATTC GATTCCCAGATCTTAACCGACTTGCCAAGA CCAGA MSH3 NM_002439 1589 TGATTACCAT 1590 CTTGTGAAAA 1591 TCCCAATTGTCG 1592 TGATTACCATCATGGCTCAGATTGGCTCCTATGTTCCTGCAGA CATGGCTCAG TGCCATCCAC CTTCTTCTGCAG AGAAGCGACAATTGGGATTGTGGATGGCATTTTCACAAG A MSH6 NM_000179 1593 TCTATTGGGG 1594 CAAATTGCGA 1595 CCGTTACCAGCT 1596 TCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCC GATTGGTAGG GTGGTGAAAT GGAAATTCCTGA TGAGAATTTCACCACTCGCAATTTG GA MTA1 NM_004689 1597 CCGCCCTCAC 1598 GGAATAAGTT 1599 CCCAGTGTCCGC 1600 CCGCCCTCACCTGCAGAGAAACGCGCTCCTTGGCGGACACTG CTGAAGAGA AGCCGCGCTT CAAGGAGCG GGGGAGGAGAGGAAGAAGCGCGGCTAACTTATTCC CT MTPN NM_145808 1601 GGTGGAAGGA 1602 CAGCAGCAGA 1603 AAGCTGCCCACA 1604 GGTGGAAGGAAACCTCTTCATTATGCAGCAGATTGTGGGCAGC AACCTCTTCA AATTCCAGG ATCTGCTGCATA TTGAAATCCTGGAATTTCTGCTGCTG MTSS1 NM_014751 1605 TTCGACAAGT 1606 CTTGGAACAT 1607 CCAAGAAACAGC 1608 TTCGACAAGTCCTCCACCATTCCAAGAAACAGCGACATCAGCC CCTCCACCAT CCGTCGGTAG GACATCAGCCAG AGTCCTACCGACGGATGTTCCAAG MUC1 NM_002456 1609 GGCCAGGATC 1610 CTCCACGTCG 1611 CTCTGGCCTTCC 1612 GGCCAGGATCTGTGGTGGTACAATTGACTCTGGCCTTCCGAG TGTGGTGGTA TGGACATTGA GAGAAGGTACC AAGGTACCATCAATGTCCACGACGTGGAG MVP NM_017458 1613 ACGAGAACGA 1614 GCATGTAGGT 1615 CGCACCTTTCCG 1616 ACGAGAACGAGGGCATCTATGTGCAGGATGTCAAGACCGGAA GGGCATCTAT GCTTCCAATC GTCTTGACATCC AGGTGCGCGCTGTGATTGGAAGCACCTACATGC GT AC T MYBL2 NM_002466 1617 GCCGAGATCG 1618 CTTTTGATGG 1619 CAGCATTGTCTG 1620 GCCGAGATCGCCAAGATGTTGCCAGGGAGGACAGACAATGCT CCAAGATG TAGAGTTCCA TCCTCCCTGGCA GTGAAGAATCACTGGAACTCTACCATCAAAAG GTGATTC MYBPC1 NM_002465 1621 CAGCAACCAG 1622 CAGCAGTAAG 1623 AAATTCGCAAGC 1624 CAGCAACCAGGGAGTCTGTACCCTGGAAATTCGCAAGCCCAG GGAGTCTGTA TGCCTCCATC CCAGCCCCTAT CCCCTATGATGGAGGCACTTACTGCTG MYC NM_002467 1625 TCCCTCCACT 1626 CGGTTGTTGC 1627 TCTGACACTGTC 1628 TCCCTCCACTCGGAAGGACTATCCTGCTGCCAAGAGGGTCAA CGGAAGGACT TGATCTGTCT CAACTTGACCCT GTTGGACAGTGTCAGAGTCCTGAGACAGATCAGCAACAACCG A CA CTT MYLK3 NM_182493 1629 CACCTGACTG 1630 GATGTAGTGC 1631 CACACCCTCACA 1632 CACCTGACTGAGCTGGATGTGGTCCTGTTCACCAGGCAGATCT AGCTGGATGT TGGTGCAGGT GATCTGCCTGGT GTGAGGGTGTGCATTACCTGCACCAGCACTACATC MYO6 NM_004999 1633 AAGCAGTTCT 1634 GATGAGCTCG 1635 CAATCCTCAGGG 1636 AAGCAGTTCTGGAGCAGGAGCGCAGGGACCGGGAGCTGGCC GGAGCAGGAG GCTTCACTCT CCAGCTCCC CTGAGGATTGCCCAGAGTGAAGCCGAGCTCATC NCAM1 NM_000615 1637 TAGTTCCCAG 1638 CAGCCTTGTT 1639 CTCAGCCTCGTC 1640 TAGTTCCCAGCTGACCATCAAAAAGGTGGATAAGAACGACGAG CTGACCATCA CTCAGCAATG GTTCTTATCCAC GCTGAGTACATCTGCATTGCTGAGAACAAGGCTG C NCAPD3 NM_015261 1641 TCGTTGCTTA 1642 CTCCAGACAG 1643 CTACTGTCCGCA 1644 TCGTTGCTTAGACAAGGCGCCTACTGTCCGCAGCAAGGCACT GACAAGGCG TGTGCAAAGC GCAAGGCACTGT GTCCAGCTTTGCACACTGTCTGGAG NCOR1 NM_006311 1645 AACCGTTACA 1646 TCTGGAGAGA 1647 CCAGGCTCAGTC 1648 AACCGTTACAGCCCAGAATCCCAGGCTCAGTCTGTCCATCATC GCCCAGAATC CCCTTGAACC TGTCCATCATCA AAAGACCAGGTTCAAGGGTCTCTCCAGA NCOR2 NM_006312 1649 CGTCATCTAC 1650 GAGCACTGGG 1651 CCTCATAGGACA 1652 CGTCATCTACGAAGGCAAGAAGGGCCACGTCTTGTCCTATGA GAAGGCAAGA TCACAGACAT AGACGTGGCCCT GGGTGGCATGTCTGTGACCCAGTGCTC NDRG1 NM_006096 1653 AGGGCAACAT 1654 CAGTGCTCCT 1655 CTGCAAGGACAC 1656 AGGGCAACATTCCACAGCTGCCCTGGCTGTGATGAGTGTCCTT TCCACAGC ACTCCGGC TCATCACAGCCA GCAGGGGCCGGAGTAGGAGCACTG NDUFS5 NM_004552 1657 AGAAGAGTCA 1658 AGGCCGAACC 1659 TGTCCAAGAAAG 1660 AGAAGAGTCAAGGGCACGAGCATCGGGTAGCCATGCCTTTCT AGGGCACGAG TTTTCTGG GCATGGCTACCC TGGACATCCAGAAAAGGTTCGGCCT NEK2 NM_002497 1661 GTGAGGCAGC 1662 TGCCAATGGT 1663 TGCCTTCCCGGG 1664 GTGAGGCAGCGCGACTCTGGCGACTGGCCGGCCATGCCTTCC GCGACTCT GTACAACACT CTGAGGACT CGGGCTGAGGACTATGAAGTGTTGTACACCATTGGCA TCA NETO2 NM_018092 1665 CCAGGGCACC 1666 AACGGTAAAT 1667 AGCCAACCCTTT 1668 CCAGGGCACCATACTGTTTCCAGCAGCCAACCCTTTTCTCCCA ATACTGTTTC CAAGGTCTTC TCTCCCATCACA TCACAACTACGAAGACCTTGATTTACCGTT GT NEXN NM_144573 1669 AGGAGGAGGA 1670 GAGCTCCTGA 1671 TCATCTTCAGCA 1672 AGGAGGAGGAAGAAGGTAGCATCATGAATGGCTCCACTGCTG AGAAGGTAGC TCTGGTTTGC GTGGAGCCATTC AAGATGAAGAGCAAACCAGATCAGGAGCTC A A NFAT5 NM_006599 1673 CTGAACCCCT 1674 AGGAAACGAT 1675 CGAGAATCAGTC 1676 CTGAACCCCTCTCCTGGTCACCGAGAATCAGTCCCCGTGGAG CTCCTGGTC GGCGAGGT CCCGTGGAGTTC TTCCCCCTCCACCTCGCCATCGTTTCCT NFATC2 NM_173091 1677 CAGTCAAGGT 1678 CTTTGGCTCG 1679 CGGGTTCCTACC 1680 CAGTCAAGGTCAGAGGCTGAGCCCGGGTTCCTACCCCACAGT CAGAGGCTGA TGGCATTC CCACAGTCATTC CATTCAGCAGCAGAATGCCACGAGCCAAAG G NFKB1 NM_003998 1681 CAGACCAAGG 1682 AGCTGCCAGT 1683 AAGCTGTAAACA 1684 CAGACCAAGGAGATGGACCTCAGCGTGGTGCGGCTCATGTTT AGATGGACCT GCTATCCG TGAGCCGCACCA ACAGCTTTTCTTCCGGATAGCACTGGCAGCT NFKBIA NM_020529 1685 CTACTGGACG 1686 CCTTGACCAT 1687 CTCGTCTTTCAT 1688 CTACTGGACGACCGCCACGACAGCGGCCTGGACTCCATGAAA ACCGCCAC CTGCTCGTAC GGAGTCCAGGCC GACGAGGAGTACGAGCAGATGGTCAAGG T NME1 NM_000269 1689 CCAACCCTGC 1690 ATGTATAATG 1691 CCTGGGACCATC 1692 CCAACCCTGCAGACTCCAAGCCTGGGACCATCCGTGGAGACT AGACTCCAA TTCCTGCCAA CGTGGAGACTTC TCTGCATACAAGTTGGCAGGAACATTATACAT CTTGTATG T NNMT NM_006169 1693 CCTAGGGCAG 1694 CTAGTCCAGC 1695 CCCTCTCCTCAT 1696 CCTAGGGCAGGGATGGAGAGAGAGTCTGGGCATGAGGAGAG GGATGGAG CAAACATCCC GCCCAGACTCTC GGTCTCGGGATGTTTGGCTGGACTAG NOS3 NM_000603 1697 ATCTCCGCCT 1698 TCGGAGCCAT 1699 TTCACTCGCTTC 1700 ATCTCCGCCTCGCTCATGGGCACGGTGATGGCGAAGCGAGTG CGCTCATG ACAGGATTGT GCCATCACCG AAGGCGACAATCCTGTATGGCTCCGA C NOX4 NM_016931 1701 CCTCAACTGC 1702 TGCTTGGAAC 1703 CCGAACACTCTT 1704 CCTCAACTGCAGCCTTATCCTTTTACCCATGTGCCGAACACTC AGCCTTATCC CTTCTGTGAT GGCTTACCTCCG TTGGCTTACCTCCGAGGATCACAGAAGGTTCCAAGCA NPBWR1 NM_005285 1705 TCACCAACCT 1706 GATGTTGATG 1707 ATCGCCGACGAG 1708 TCACCAACCTGTTCATCCTCAACCTGGCCATCGCCGACGAGCT GTTCATCCTC GGCAGCAC CTCTTCACG CTTCACGCTGGTGCTGCCCATCAACATC NPM1 NM_002520 1709 AATGTTGTCC 1710 CAAGCAAAGG 1711 AACAGGCATTTT 1712 AATGTTGTCCAGGTTCTATTGCCAAGAATGTGTTGTCCAAAAT AGGTTCTATT GTGGAGTTC GGACAACACATT GCCTGTTTAGTTTTTAAAGATGGAACTCCACCCTTTGCTTG GC CTTG NRG1 NM_013957 1713 CGAGACTCTC 1714 CTTGGCGTGT 1715 ATGACCACCCCG 1716 CGAGACTCTCCTCATAGTGAAAGGTATGTGTCAGCCATGACCA CTCATAGTGA GGAAATCTAC GCTCGTATGTCA CCCCGGCTCGTATGTCACCTGTAGATTTCCACACGCCAAG AAGGTAT AG NRIP3 NM_020645 1717 CCCACAAGCA 1718 TGCTCAATCT 1719 AGCTTTCTCTAC 1720 CCCACAAGCATGAAGGAGAAAAGCTTTCTCTACCCCGGCATCT TGAAGGAGA GGCCCACTA CCCGGCATCTCA CAAAGTAGTGGGCCAGATTGAGCA NRP1 NM_003873 1721 CAGCTCTCTC 1722 CCCAGCAGCT 1723 CAGGATCTACCC 1724 CAGCTCTCTCCACGCGATTCATCAGGATCTACCCCGAGAGAG CACGCGATTC CCATTCTGA CGAGAGAGCCAC CCACTCATGGCGGACTGGGGCTCAGAATGGAGCTGCTGGG TCAT NUP62 NM_153719 1725 AGCCTCTTTG 1726 CTGTGGTCAC 1727 TCATCTGCCACC 1728 AGCCTCTTTGCGTCAATAGCAACTGCTCCAACCTCATCTGCCA CGTCAATAGC AGGGGTACAG ACTGGACTCTCC CCACTGGACTCTCCCTCTGTACCCCTGTGACCACAG OAZ1 NM_004152 1729 AGCAAGGACA 1730 GAAGACATGG 1731 CTGCTCCTCAGC 1732 AGCAAGGACAGCTTTGCAGTTCTCCTGGAGTTCGCTGAGGAG GCTTTGCAGT TCGGCTCG GAACTCCAGGAG CAGCTGCGAGCCGACCATGTCTTC OCLN NM_002538 1733 CCCTCCCATC 1734 GACGCGGGAG 1735 CTCCTCCCTCGG 1736 CCCTCCCATCCGAGTTTCAGGTGAATTGGTCACCGAGGGAGG CGAGTTTC TGTAGGTG TGACCAATTCAC AGGCCGACACACCACACCTACACTCCCGCGTC ODC1 NM_002539 1737 AGAGATCACC 1738 CGGGCTCAGC 1739 CCAGCGTTGGAC 1740 AGAGATCACCGGCGTAATCAACCCAGCGTTGGACAAATACTTT GGCGTAATCA TATGATTCTC AAATACTTTCCG CCGTCAGACTCTGGAGTGAGAATCATAGCTGAGCCCG A A TCA OLFML2B NM_015441 1741 CATGTTGGAA 1742 CACCAGTTTG 1743 TGGCCTGGATCT 1744 CATGTTGGAAGGAGCGTTCTATGGCCTGGATCTCCTGAAGCTA GGAGCGTTCT GTGGTGACTG CCTGAAGCTACA CATTCAGTCACCACCAAACTGGTG OLFML3 NM_020190 1745 TCAGAACTGA 1746 CCAGATAGTC 1747 CAGACGATCCAC 1748 TCAGAACTGAGGCCGACACCATCTCCGGGAGAGTGGATCGTC GGCCGACAC TACCTCCCGC TCTCCCGGAGAT TGGAGCGGGAGGTAGACTATCTGG T OMD NM_005014 1749 CGCAAACTCA 1750 CAGTCACAGC 1751 TCCGATGCACAT 1752 CGCAAACTCAAGACTATCCCAAATATTCCGATGCACATTCAGC AGACTATCCC CTCAATTTCA TCAGCAACTCTA AACTCTACCTTCAGTTCAATGAAATTGAGGCTGTGACTG A TT CC OR51E1 NM_152430 1753 GCATGCTTTC 1754 AGAAGATGGC 1755 TCCTCATCTCCA 1756 GCATGCTTTCAGGCATTGACATCCTCATCTCCACCTCATCCAT AGGCATTGA CAGCATTTTG CCTCATCCATGC GCCCAAAATGCTGGCCATCTTCT OR51E2 NM_030774 1757 TATGGTGCCA 1758 GTCCTTGTCA 1759 ACATAGCCAGCA 1760 TATGGTGCCAAAACCAAACAGATCAGAACACGGGTGCTGGCT AAACCAAACA CAGCTGATCT CCCGTGTTCTGA ATGTTCAAGATCAGCTGTGACAAGGAC TG OSM NM_020530 1761 GTTTCTGAAG 1762 AGGTGTCTGG 1763 CTGAGCTGGCCT 1764 GTTTCTGAAGGGGAGGTCACAGCCTGAGCTGGCCTCCTATGC GGGAGGTCAC TTTGGGACA CCTATGCCTCAT CTCATCATGTCCCAAACCAGACACCT PAGE1 NM_003785 1765 CAACCTGACG 1766 CAGATGCTCC 1767 CCAACTCAAAGT 1768 CAACCTGACGAAGTGGAATCACCAACTCAAAGTCAGGATTCTA AAGTGGAATC CTCATCCTCT CAGGATTCTACA CACCTGCTGAAGAGAGAGAGGATGAGGGAGCATCTG CCTGC PAGE4 NM_007003 1769 GAATCTCAGC 1770 GTTCTTCGAT 1771 CCAACTGACAAT 1772 GAATCTCAGCAAGAGGAACCACCAACTGACAATCAGGATATTG AAGAGGAACC CGGAGGTGTT CAGGATATTGAA AACCTGGACAAGAGAGAGAAGGAACACCTCCGATCGAAGAAC A CCTGG PAK6 NM_020168 1773 CCTCCAGGTC 1774 GTCCCTTCAG 1775 AGTTTCAGGAAG 1776 CCTCCAGGTCACCCACAGCCAGTTTCAGGAAGGCTGCCCCTC ACCCACAG GCCAGAACTT GCTGCCCCTCTC TCTCCCACTAAGTTCTGGCCTGAAGGGAC PATE1 NM_138294 1777 TGGTAATCCC 1778 TCCACCTTAT 1779 CAGCACAGTTCT 1780 TGGTAATCCCTGGTTAACCTTCATGGGCTGCCTAAAGAACTGT TGGTTAACCT GCCTTTCACA TTAGGCAGCCCA GCTGATGTGAAAGGCATAAGGTGGA TC PCA3 NR_015342 1781 CGTGATTGTC 1782 AGAAAGGGGA 1783 CTGAGATGCTCC 1784 CGTGATTGTCAGGAGCAAGACCTGAGATGCTCCCTGCCTTCAG AGGAGCAAGA GATGCAGAGG CTGCCTTCAGTG TGTCCTCTGCATCTCCCCTTTCT PCDHGB7 NM_018927 1785 CCCAGCGTTG 1786 GAAACGCCAG 1787 ATTCTTAAACAG 1788 CCCAGCGTTGAAGCAGATAAGAAGATTCTTAAACAGCAAGCCC AAGCAGAT TCCGTGTT CAAGCCCCGCC CGCCCAACACGGACTGGCGTTTC PCNA NM_002592 1789 GAAGGTGTTG 1790 GGTTTACACC 1791 ATCCCAGCAGGC 1792 GAAGGTGTTGGAGGCACTCAAGGACCTCATCAACGAGGCCTG GAGGCACTCA GCTGGAGCTA CTCGTTGATGAG CTGGGATATTAGCTCCAGCGGTGTAAACC AG A PDE9A NM_ 1793 TTCCACAACT 1794 AGACTGCAGA 1795 TACATCATCTGG 1796 TTCCACAACTTCCGGCACTGCTTCTGCGTGGCCCAGATGATGT 001001570 TCCGGCAC GCCAGACCA GCCACGCAGAAG ACAGCATGGTCTGGCTCTGCAGTCT PDGFRB NM_002609 1797 CCAGCTCTCC 1798 GGGTGGCTCT 1799 ATCAATGTCCCT 1800 CCAGCTCTCCTTCCAGCTACAGATCAATGTCCCTGTCCGAGTG TTCCAGCTAC CACTTAGCTC GTCCGAGTGCTG CTGGAGCTAAGTGAGAGCCACCC PECAM1 NM_000442 1801 TGTATTTCAA 1802 TTAGCCTGAG 1803 TTTATGAACCTG 1804 TGTATTTCAAGACCTCTGTGCACTTATTTATGAACCTGCCCTG GACCTCTGTG GAATTGCTGT CCCTGCTCCCAC CTCCCACAGAACACAGCAATTCCTCAGGCTAA CACTT GTT A PEX10 NM_153818 1805 GGAGAAGTTC 1806 ATCTGTGTCC 1807 CTACCTTCGGCA 1808 GGAGAAGTTCCCTCCCCAGAAGCTCATCTACCTTCGGCACTAC CCTCCCCAG AGGCCCAC CTACCGCTGAGC CGCTGAGCCGGCGCCCGGGTGGGCCTGGACACAGAT PGD NM_002631 1809 ATTCCCATGC 1810 CTGGCTGGAA 1811 ACTGCCCTCTCC 1812 ATTCCCATGCCCTGTTTTACCACTGCCCTCTCCTTCTATGACG CCTGTTTTAC GCATCTCAT TTCTATGACGGG GGTACAGACATGAGATGCTTCCAGCCAG T PGF NM_002632 1813 GTGGTTTTCC 1814 AGCAAGGGAA 1815 ATCTTCTCAGAC 1816 GTGGTTTTCCCTCGGAGCCCCCTGGCTCGGGACGTCTGAGAA CTCGGAGC CAGCCTCAT GTCCCGAGCCAG GATGCCGGTCATGAGGCTGTTCCCTTGCT PGK1 NM_000291 1817 AGAGCCAGTT 1818 CTGGGCCTAC 1819 TCTCTGCTGGGC 1820 AGAGCCAGTTGCTGTAGAACTCAAATCTCTGCTGGGCAAGGAT GCTGTAGAAC ACAGTCCTTC AAGGATGTTCTG GTTCTGTTCTTGAAGGACTGTGTAGGCCCAG TCAA A TTC PGR NM_000926 1821 GATAAAGGAG 1822 TCACAAGTCC 1823 TAAATTGCCGTC 1824 GATAAAGGAGCCGCGTGTCACTAAATTGCCGTCGCAGCCGCA CCGCGTGTCA GGCACTTGAG GCAGCCGCA GCCACTCAAGTGCCGGACTTGTGA PHTF2 NM_020432 1825 GATATGGCTG 1826 GGTTTGGGTG 1827 ACAATCTGGCAA 1828 GATATGGCTGATGCTGCTCCTGGGAACTGTGCATTGCCAGATT ATGCTGCTCC TTCTTGTGGA TGCACAGTTCCC GTTTCCACAAGAACACCCAAACC PIK3C2A NM_002645 1829 ATACCAATCA 1830 CACACTAGCA 1831 TGTGCTGTGACT 1832 ATACCAATCACCGCACAAACCCAGGCTATTTGTTAAGTCCAGT CCGCACAAAC TTTTCTCCGC GGACTTAACAAA CACAGCACAAAGAAACATATGCGGAGAAAATGCTAGTGTG C ATA TAGCCT PIK3CA NM_006218 1833 GTGATTGAAG 1834 GTCCTGCGTG 1835 TCCTGCTTCTCG 1836 GTGATTGAAGAGCATGCCAATTGGTCTGTATCCCGAGAAGCAG AGCATGCCAA GGAATAGC GGATACAGACCA GATTTAGCTATTCCCACGCAGGAC PIK3CG NM_002649 1837 GGAGAACTCA 1838 TGATGCTTAG 1839 TTCTGGACAATT 1840 GGAGAACTCAATGTCCATCTCCATTCTTCTGGACAATTACTGC ATGTCCATCT GCAGGGCT ACTGCCACCCGA CACCCGATAGCCCTGCCTAAGCATCA CC PIM1 NM_002648 1841 CTGCTCAAGG 1842 GGATCCACTC 1843 TACACTCGGGTC 1844 CTGCTCAAGGACACCGTCTACACGGACTTCGATGGGACCCGA ACACCGTCTA TGGAGGGC CCATCGAAGTCC GTGTATAGCCCTCCAGAGTGGATCC PLA2G7 NM_005084 1845 CCTGGCTGTG 1846 TGACCCATGC 1847 TGGCAATACATA 1848 CCTGGCTGTGGTTTATCCTTTTGACTGGCAATACATAAATCCT GTTTATCCTT TGATGATTTC AATCCTGTTGCC GTTGCCCATATGAAATCATCAGCATGGGTCA CA PLAU NM_002658 1849 GTGGATGTGC 1850 CTGCGGATCC 1851 AAGCCAGGCGTC 1852 GTGGATGTGCCCTGAAGGACAAGCCAGGCGTCTACACGAGAG CCTGAAGGA AGGGTAAGAA TACACGAGAGTC TCTCACACTTCTTACCCTGGATCCGCAG TCAC PLAUR NM_002659 1853 CCCATGGATG 1854 CCGGTGGCTA 1855 CATTGACTGCCG 1856 CCCATGGATGCTCCTCTGAAGAGACTTTCCTCATTGACTGCCG CTCCTCTGAA CCAGACATTG AGGCCCCATG AGGCCCCATGAATCAATGTCTGGTAGCCACCGG PLG NM_000301 1857 GGCAAAATTT 1858 ATGTATCCAT 1859 TGCCAGGCCTGG 1860 GGCAAAATTTCCAAGACCATGTCTGGACTGGAATGCCAGGCCT CCAAGACCAT GAGCGTGTGG GACTCTCA GGGACTCTCAGAGCCCACACGCTCATGGATACAT PLK1 NM_005030 1861 AATGAATACA 1862 TGTCTGAAGC 1863 AACCCCGTGGCC 1864 AATGAATACAGTATTCCCAAGCACATCAACCCCGTGGCCGCCT GTATTCCCAA ATCTTCTGGA GCCTCC CCCTCATCCAGAAGATGCTTCAGACA GCACAT TGA PLOD2 NM_000935 1865 CAGGGAGGTG 1866 TCTCCCAGGA 1867 TCCAGCCTTTTC 1868 CAGGGAGGTGGTTGCAAATTTCTAAGGTACAATTGCTCTATTG GTTGCAAAT TGCATGAAG GTGGTGACTCAA AGTCACCACGAAAAGGCTGGAGCTTCATGCATCCTGGGAGA PLP2 NM_002668 1869 CCTGATCTGC 1870 GCAGCAAGGA 1871 ACACCAGGCTAC 1872 CCTGATCTGCTTCAGTGCCTCCACACCAGGCTACTCCTCCCTG TTCAGTGCC TCATCTCAAT TCCTCCCTGTCG TCGGTGATTGAGATGATCCTTGCTGC C PNLIPRP2 NM_005396 1873 TGGAGAAGGT 1874 CACGGCTTGG 1875 ACCCGTGCCTCC 1876 TGGAGAAGGTGAACTGCATCTGTGTGGACTGGAGGCACGGGT GAACTGCATC GTGTACATT AGTCCACAC CCCGGGCAATGTACACCCAAGCCGTG POSTN NM_006475 1877 GTGGCCCAAT 1878 TCACAGGTGC 1879 TTCTCCATCTGG 1880 GTGGCCCAATTAGGCTTGGCATCTGCTCTGAGGCCAGATGGA TAGGCTTG CAGCAAAG CCTCAGAGCAGA GAATACACTTTGCTGGCACCTGTGA PPAP2B NM_003713 1881 ACAAGCACCA 1882 CACGAAGAAA 1883 ACCAGGGCTCCT 1884 ACAAGCACCATCCCAGTGATGTTCTGGCAGGATTTGCTCAAGG TCCCAGTGA ACTATGCAGC TGAGCAAATCCT AGCCCTGGTGGCCTGCTGCATAGTTTTCTTCGTG AG PPFIA3 NM_003660 1885 CCTGGAGCTC 1886 AGCCACATAG 1887 CACCCACTTTAC 1888 CCTGGAGCTCCGTTACTCTCAGGCACCCACTTTACCTTCTGGT CGTTACTCTC GGATCCAGG CTTCTGGTGCCC GCCCACCTGGATCCCTATGTGGCT PPP1R12A NM_002480 1889 CGGCAAGGGG 1890 TGCCTGGCAT 1891 CCGTTCTTCTTC 1892 CGGCAAGGGGTTGATATAGAAGCAGCTCGAAAGGAAGAAGAA TTGATATAGA CTCTAAGCA CTTTCGAGCTGC CGGATCATGCTTAGAGATGCCAGGCA PPP3CA NM_000944 1893 ATACTCCGAG 1894 GGAAGCCTGT 1895 TACATGCGGTAC 1896 ATACTCCGAGCCCACGAAGCCCAAGATGCAGGGTACCGCATG CCCACGAA TGTTTGGC CCTGCATCTTGG TACAGGAAAAGCCAAACAACAGGCTTCC PRIMA1 NM_178013 1897 ATCCTCTTCC 1898 CCCAGCTGAG 1899 TGACGCATCCAG 1900 ATCCTCTTCCCTGAGCCGCTGACGCATCCAGGGCTCTAGTCTG CTGAGCCG AGGGAATTTA GGCTCTAGTCTG CACATAAATTCCCTCTCAGCTGGG PRKAR1B NM_002735 1901 ACAAAACCAT 1902 TGTCATCCAG 1903 AAGGCCATCTCC 1904 ACAAAACCATGACTGCGCTGGCCAAGGCCATCTCCAAGAACG GACTGCGCT GTGAGCGA AAGAACGTGCTC TGCTCTTCGCTCACCTGGATGACA PRKAR2B NM_002736 1905 TGATAATCGT 1906 GCACCAGGAG 1907 CGAACTGGCCTT 1908 TGATAATCGTGGGAGTTTCGGCGAACTGGCCTTAATGTACAAT GGGAGTTTCG AGGTAGCAGT AATGTACAATAC ACACCCAGAGCAGCTACAATCACTGCTACCTCTCCTGGTGC ACCCA PRKCA NM_002737 1909 CAAGCAATGC 1910 GTAAATCCGC 1911 CAGCCTCTGCGG 1912 CAAGCAATGCGTCATCAATGTCCCCAGCCTCTGCGGAATGGAT GTCATCAATG CCCCTCTTCT AATGGATCACAC CACACTGAGAAGAGGGGGCGGATTTAC T T PRKCB NM_002738 1913 GACCCAGCTC 1914 CCCATTCACG 1915 CCAGACCATGGA 1916 GACCCAGCTCCACTCCTGCTTCCAGACCATGGACCGCCTGTA CACTCCTG TACTCCATCA CCGCCTGTACTT CTTTGTGATGGAGTACGTGAATGGG PROM1 NM_006017 1917 CTATGACAGG 1918 CTCCAACCAT 1919 ACCCGAGGCTGT 1920 CTATGACAGGCATGCCACCCCGACCACCCGAGGCTGTGTCTC CATGCCACC GAGGAAGACG GTCTCCAACAC CAACACCGGAGGCGTCTTCCTCATGGTTGGAG PROS1 NM_000313 1921 GCAGCACAGG 1922 CCCACCTATC 1923 CTCATCCTGACA 1924 GCAGCACAGGAATCTTCTTCTTGGCAGCTGCAGTCTGTCAGGA AATCTTCTTC CAACCTAATC GACTGCAGCTGC TGAGATATCAGATTAGGTTGGATAGGTGGG TT TG PSCA NM_005672 1925 ACCGTCATCA 1926 CGTGATGTTC 1927 CCTGTGAGTCAT 1928 ACCGTCATCAGCAAAGGCTGCAGCTTGAACTGCGTGGATGAC GCAAAGGCT TTCTTGCCC CCACGCAGTTCA TCACAGGACTACTACGTGGGCAAGAAGAACATCACG PSMD13 NM_002817 1929 GGAGGAGCTC 1930 CGGATCCTGC 1931 CCTGAAGTGTCA 1932 GGAGGAGCTCTACACGAAGAAGTTGTGGCATCAGCTGACACT TACACGAAGA ACAAAATCA GCTGATGCCACA TCAGGTGCTTGATTTTGTGCAGGATCCG AG PTCH1 NM_000264 1933 CCACGACAAA 1934 TACTCGATGG 1935 CCTGAAACAAGG 1936 CCACGACAAAGCCGACTACATGCCTGAAACAAGGCTGAGAAT GCCGACTAC GCTCTGCTG CTGAGAATCCCG CCCGGCAGCAGAGCCCATCGAGTA PTEN NM_000314 1937 TGGCTAAGTG 1938 TGCACATATC 1939 CCTTTCCAGCTT 1940 TGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTA AAGATGACAA ATTACACCAG TACAGTGAATTG AAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCA TCATG TTCGT CTGCA PTGER3 NM_000957 1941 TAACTGGGGC 1942 TTGCAGGAAA 1943 CCTTTGCCTTCC 1944 TAACTGGGGCAACCTTTTCTTCGCCTCTGCCTTTGCCTTCCTG AACCTTTTCT AGGTGACTGT TGGGGCTCTT GGGCTCTTGGCGCTGACAGTCACCTTTTCCTGCAA PTGS2 NM_000963 1945 GAATCATTCA 1946 CTGTACTGCG 1947 CCTACCACCAGC 1948 GAATCATTCACCAGGCAAATTGCTGGCAGGGTTGCTGGTGGTA CCAGGCAAAT GGTGGAACAT AACCCTGCCA GGAATGTTCCACCCGCAGTACAG TG PTH1R NM_000316 1949 CGAGGTACAA 1950 GCGTGCCTTT 1951 CCAGTGCCAGTG 1952 CGAGGTACAAGCTGAGATCAAGAAATCTTGGAGCCGCTGGAC GCTGAGATCA CGCTTGAA TCCAGCGGCT ACTGGCACTGGACTTCAAGCGAAAGGCACGC AGAA PTHLH NM_002820 1953 AGTGACTGGG 1954 AAGCCTGTTA 1955 TGACACCTCCAC 1956 AGTGACTGGGAGTGGGCTAGAAGGGGACCACCTGTCTGACAC AGTGGGCTAG CCGTGAATCG AACGTCGCTGGA CTCCACAACGTCGCTGGAGCTCGATTCACGGTAACAGGCTT AA A PTK2 NM_005607 1957 GACCGGTCGA 1958 CTGGACATCT 1959 ACCAGGCCCGTC 1960 GACCGGTCGAATGATAAGGTGTACGAGAATGTGACGGGCCTG ATGATAAGGT CGATGACAGC ACATTCTCGTAC GTGAAAGCTGTCATCGAGATGTCCAG PTK2B NM_004103 1961 CAAGCCCAGC 1962 GAACCTGGAA 1963 CTCCGCAAACCA 1964 CAAGCCCAGCCGACCTAAGTACAGACCCCCTCCGCAAACCAA CGACCTAAG CTGCAGCTTT ACCTCCTGGCT CCTCCTGGCTCCAAAGCTGCAGTTCCAGGTTC G PTK6 NM_005975 1965 GTGCAGGAAA 1966 GCACACACGA 1967 AGTGTCTGCGTC 1968 GTGCAGGAAAGGTTCACAAATGTGGAGTGTCTGCGTCCAATAC GGTTCACAAA TGGAGTAAGG CAATACACGCGT ACGCGTGTGCTCCTCTCCTTACTCCATCGTGTGTGC PTK7 NM_002821 1969 TCAGAGGACT 1970 CATACACCTC 1971 CGCAAGGTCCCA 1972 TCAGAGGACTCACGGTTCGAGGTCTTCAAGAATGGGACCTTGC CACGGTTCG CACGCTGTTG TTCTTGAAGACC GCATCAACAGCGTGGAGGTGTATG PTPN1 NM_002827 1973 AATGAGGAAG 1974 CTTCGATCAC 1975 CTGATCCAGACA 1976 AATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGCCGACCA TTTCGGATGG AGCCAGGTAG GCCGACCAGCT GCTGCGCTTCTCCTACCTGGCTGTGATCGAAG PTPRK NM_002844 1977 TCAAACCCTC 1978 AGCAGCCAGT 1979 CCCCATCGTTGT 1980 TCAAACCCTCCCAGTGCTGGCCCCATCGTTGTACATTGCAGTG CCAGTGCT TCGTCCAG ACATTGCAGTGC CTGGTGCTGGACGAACTGGCTGCT PTTG1 NM_004219 1981 GGCTACTCTG 1982 GCTTCAGCCC 1983 CACACGGGTGCC 1984 GGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGC ATCTATGTTG ATCCTTAGCA TGGTTCTCCA ACCCGTGTGGTTGCTAAGGATGGGCTGAAGC ATAAGGAA PYCARD NM_013258 1985 CTTTATAGAC 1986 AGCATCCAGC 1987 ACGTTTGTGACC 1988 CTTTATAGACCAGCACCGGGCTGCGCTTATCGCGAGGGTCAC CAGCACCGGG AGCCACTC CTCGCGATAAGC AAACGTTGAGTGGCTGCTGGATGCT RAB27A NM_004580 1989 TGAGAGATTA 1990 CCGGATGCTT 1991 ACAAATTGCTTC 1992 TGAGAGATTAATGGGCATTGTGTACAAATTGCTTCTCACCATC ATGGGCATTG TATTCGTAGG TCACCATCCCCA CCCATTAGACCTACGAATAAAGCATCCGG TG TT RAB30 NM_014488 1993 TAAAGGCTGA 1994 CTCCCCAGCA 1995 CCATCAGGGCAG 1996 TAAAGGCTGAGGCACGGAGAAGAAAAGGAATCAGCAACTGCC GGCACGGA TCTCATGG TTGCTGATTCCT CTGATGGGCCATGAGATGCTGGGGAG RAB31 NM_006868 1997 CTGAAGGACC 1998 ATGCAAAGCC 1999 CTTCTCAAAGTG 2000 CTGAAGGACCCTACGCTCGGTGGCCTGGCACCTCACTTTGAG CTACGCTCG AGTGTGCTC AGGTGCCAGGCC AAGAGTGAGCACACTGGCTTTGCAT RAD21 NM_006265 2001 TAGGGATGGT 2002 TCGCGTACAC 2003 CACTTAAAACGA 2004 TAGGGATGGTATCTGAAACAACAATGGTCACCCTCTTGAGATT ATCTGAAACA CTCTGCTC ATCTCAAGAGGG CGTTTTAAGTGTAATTCCATAATGAGCAGAGGTGTACGCGA ACA TGACCA RAD51 NM_002875 2005 AGACTACTCG 2006 AGCATCCGCA 2007 CTTTCAGCCAGG 2008 AGACTACTCGGGTCGAGGTGAGCTTTCAGCCAGGCAGATGCA GGTCGAGGTG GAAACCTG CAGATGCACTTG CTTGGCCAGGTTTCTGCGGATGCT RAD9A NM_004584 2009 GCCATCTTCA 2010 CGGTGTCTGA 2011 CTTTGCTGGACG 2012 GCCATCTTCACCATCAAGGACTCTTTGCTGGACGGCCACTTTG CCATCAAGG GAGTGTGGC GCCACTTTGTCT TCTTGGCCACACTCTCAGACACCG RAF1 NM_002880 2013 CGTCGTATGC 2014 TGAAGGCGTG 2015 TCCAGGATGCCT 2016 CGTCGTATGCGAGAGTCTGTTTCCAGGATGCCTGTTAGTTCTC GAGAGTCTGT AGGTGTAGAA GTTAGTTCTCAG AGCACAGATATTCTACACCTCACGCCTTCA CA RAGE NM_014226 2017 ATTAGGGGAC 2018 GGGTGGAGAT 2019 CCGGAGTGTCTA 2020 ATTAGGGGACTTTGGCTCCTGCCGGAGTGTCTATTCCAAGCAG TTTGGCTCCT GTATTCCGTG TTCCAAGCAGCC CCGTACACGGAATACATCTCCACCC RALA NM_005402 2021 TGGTCCTGAA 2022 CCCCATTTCA 2023 TTGTGTTTCTTG 2024 TGGTCCTGAATGTAGCGTGTAAGCTTGTGTTTCTTGGGCAGTC TGTAGCGTGT CCTCTTCAAT GGCAGTCTTTCT TTTCTTGAAATTGAAGAGGTGAAATGGGG TGAA RALBP1 NM_006788 2025 GGTGTCAGAT 2026 TTCGATATTG 2027 TGCTGTCCTGTC 2028 GGTGTCAGATATAAATGTGCAAATGCCTTCTTGCTGTCCTGTC ATAAATGTGC CCAGCAGCTA GGTCTCAGTACG GGTCTCAGTACGTTCACTTTATAGCTGCTGGCAATATCGAA AAATGC TAAA TTCA RAP1B NM_ 2029 TGACAGCGTG 2030 CTGAGCCAAG 2031 CACGCATGATGC 2032 TGACAGCGTGAGAGGTACTAGGTTTTGACAAGCTTGCATCATG 001010942 AGAGGTACTA AACGACTAGC AAGCTTGTCAAA CGTGAGTATAAGCTAGTCGTTCTTGGCTCAG GG TT RARB NM_000965 2033 ATGAACCCTT 2034 GAGCTGGGTG 2035 TGTGCTCTGCTG 2036 ATGAACCCTTGACCCCAAGTTCAAGTGGGAACACAGCAGAGC GACCCCAAGT AGATGCTAGG TGTTCCCACTTG ACAGTCCTAGCATCTCACCCAGCTC RASSF1 NM_007182 2037 AGGGCACGTG 2038 AAAGAGTGCA 2039 CACCACCAAGAA 2040 AGGGCACGTGAAGTCATTGAGGCCCTGCTGCGAAAGTTCTTG AAGTCATTG AACTTGCGG CTTTCGCAGCAG GTGGTGGATGACCCCCGCAAGTTTGCACTCTTT RB1 NM_000321 2041 CGAAGCCCTT 2042 GGACTCTTCA 2043 CCCTTACGGATT 2044 CGAAGCCCTTACAAGTTTCCTAGTTCACCCTTACGGATTCCTG ACAAGTTTCC GGGGTGAAAT CCTGGAGGGAAC GAGGGAACATCTATATTTCACCCCTGAAGAGTCC RECK NM_021111 2045 GTCGCCGAGT 2046 GTGGGATGAT 2047 TCAAGTGTCCTT 2048 GTCGCCGAGTGTGCTTCTGTCAAGTGTCCTTCGCTCTTGGCAG GTGCTTCT GGGTTTGC CGCTCTTGGCAG CTGGATGCAAACCCATCATCCCAC REG4 NM_032044 2049 TGCTAACTCC 2050 TGCTAGGTTT 2051 TCCTCTTCCTTT 2052 TGCTAACTCCTGCACAGCCCCGTCCTCTTCCTTTCTGCTAGCC TGCACAGCC CCCCTCTGAA CTGCTAGCCTGG TGGCTAAATCTGCTCATTATTTCAGAGGGGAAACCTAGCA C RELA NM_021975 2053 CTGCCGGGAT 2054 CCAGGTTCTG 2055 CTGAGCTCTGCC 2056 CTGCCGGGATGGCTTCTATGAGGCTGAGCTCTGCCCGGACCG GGCTTCTAT GAAACTGTGG CGGACCGCT CTGCATCCACAGTTTCCAGAACCTGG AT RFX1 NM_002918 2057 TCCTCTCCAA 2058 CAGGCCCTGG 2059 TCCAATGGACCA 2060 TCCTCTCCAAGTTCGAGCCCGTGCTCCAATGGACCAAGCACTG GTTCGAGCC TACAGCAC AGCACTGTGACA TGACAACGTGCTGTACCAGGGCCTG RGS10 NM_ 2061 AGACATCCAC 2062 CCATTTGGCT 2063 AGTTCCAGCAGC 2064 AGACATCCACGACAGCGATGGCAGTTCCAGCAGCAGCCACCA 001005339 GACAGCGAT GTGCTCTTG AGCCACCAGAG GAGCCTCAAGAGCACAGCCAAATGG RGS7 NM_002924 2065 CAGGCTGCAG 2066 TTTGCTTGTG 2067 TGAAAATGAACT 2068 CAGGCTGCAGAGAGCATTTGCCCGGAAGTGGGAGTTCATTTTC AGAGCATTT CTTCTGCTTG CCCACTTCCGGG ATGCAAGCAGAAGCACAAGCAAA RHOA NM_001664 2069 TGGCATAGCT 2070 TGCCACAGCT 2071 AAATGGGCTCAA 2072 TGGCATAGCTCTGGGGTGGGCAGTTTTTTGAAAATGGGCTCAA CTGGGGTG GCATGAAC CCAGAAAAGCCC CCAGAAAAGCCCAAGTTCATGCAGCTGTGGCA RHOB NM_004040 2073 AAGCATGAAC 2074 CCTCCCCAAG 2075 CTTTCCAACCCC 2076 AAGCATGAACAGGACTTGACCATCTTTCCAACCCCTGGGGAAG AGGACTTGAC TCAGTTGC TGGGGAAGACAT ACATTTGCAACTGACTTGGGGAGG C RHOC NM_175744 2077 CCCGTTCGGT 2078 GAGCACTCAA 2079 TCCGGTTCGCCA 2080 CCCGTTCGGTCTGAGGAAGGCCGGGACATGGCGAACCGGATC CTGAGGAA GGTAGCCAAA TGTCCCG AGTGCCTTTGGCTACCTTGAGTGCTC GG RLN1 NM_006911 2081 AGCTGAAGGC 2082 TTGGAATCCT 2083 TGAGAGGCAACC 2084 AGCTGAAGGCAGCCCTATCTGAGAGGCAACCATCATTACCAG AGCCCTATC TTAATGCAGG ATCATTACCAGA AGCTACAGCAGTATGTACCTGCATTAAAGGATTCCAA T GC RND3 NM_005168 2085 TCGGAATTGG 2086 CTGGTTACTC 2087 TTTTAAGCCTGA 2088 TCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAA ACTTGGGAG CCCTCCAACA CTCCTCACCGCG AACTTGTTGGAGGGGAGTAACCAG RNF114 NM_018683 2089 TGACAGGGGA 2090 GGAAGACAGC 2091 CCAGGTCAGCCC 2092 TGACAGGGGAAGTGGGTCCCCAGGTCAGCCCTTCTCTTCCCT AGTGGGTC TTTGGCAAGA TTCTCTTCCCTT TTGGGCTCTTGCCAAAGCTGTCTTCC ROBO2 NM_002942 2093 CTACAAGGCC 2094 CACCAGTGGC 2095 CTGTACCATCCA 2096 CTACAAGGCCCAGCCAACCAAACGCTGGCAGTGGATGGTACA CAGCCAAC TTTACATTTC CTGCCAGCGTTT GCGTTACTGAAATGTAAAGCCACTGGTG AG RRM1 NM_001033 2097 GGGCTACTGG 2098 CTCTCAGCAT 2099 CATTGGAATTGC 2100 GGGCTACTGGCAGCTACATTGCTGGGACTAATGGCAATTCCAA CAGCTACATT CGGTACAAGG CATTAGTCCCAG TGGCCTTGTACCGATGCTGAGAG C RRM2 NM_001034 2101 CAGCGGGATT 2102 ATCTGCGTTG 2103 CCAGCACAGCCA 2104 CAGCGGGATTAAACAGTCCTTTAACCAGCACAGCCAGTTAAAA AAACAGTCCT AAGCAGTGAG GTTAAAAGATGC GATGCAGCCTCACTGCTTCAACGCAGAT A S100P NM_005980 2105 AGACAAGGAT 2106 GAAGTCCACC 2107 TTGCTCAAGGAC 2108 AGACAAGGATGCCGTGGATAAATTGCTCAAGGACCTGGACGC GCCGTGGATA TGGGCATCTC CTGGACGCCAA CAATGGAGATGCCCAGGTGGACTTC A SAT1 NM_002970 2109 CCTTTTACCA 2110 ACAATGCTGT 2111 TCCAGTGCTCTT 2112 CCTTTTACCACTGCCTGGTTGCAGAAGTGCCGAAAGAGCACTG CTGCCTGGTT GTCCTTCCG TCGGCACTTCTG GACTCCGGAAGGACACAGCATTGT SCUBE2 NM_020974 2113 TGACAATCAG 2114 TGTGACTACA 2115 CAGGCCCTCTTC 2116 TGACAATCAGCACACCTGCATTCACCGCTCGGAAGAGGGCCT CACACCTGCA GCCGTGATCC CGAGCGGT GAGCTGCATGAATAAGGATCACGGCTGTAGTCACA T TTA SDC1 NM_002997 2117 GAAATTGACG 2118 AGGAGCTAAC 2119 CTCTGAGCGCCT 2120 GAAATTGACGAGGGGTGTCTTGGGCAGAGCTGGCTCTGAGCG AGGGGTGTCT GGAGAACCTG CCATCCAAGG CCTCCATCCAAGGCCAGGTTCTCCGTTAGCTCCT SDC2 NM_002998 2121 GGATTGAAGT 2122 ACCAGCCACA 2123 AACTCCATCTCC 2124 GGATTGAAGTGGCTGGAAAGAGTGATGCCTGGGGAAGGAGAT GGCTGGAAAG GTACCCTCA TTCCCCAGGCAT GGAGTTATGAGGGTACTGTGGCTGGT SDHC NM_003001 2125 CTTCCCTCGG 2126 TTCCCTCCTG 2127 TTACATCCTCCC 2128 CTTCCCTCGGGTCTCAGGCATTTACATCCTCCCTCTCCCCGCA GTCTCAGG GTAAAGGTCA TCTCCCCGCAAT ATCTGACCTTTACCAGGAGGGAA SEC14L1 NM_ 2129 AGGGTTCCCA 2130 GCAGGCATGC 2131 CGGGCTTCTACA 2132 AGGGTTCCCATGTGACCAGGTGGCCGGGCTTCTACATCCTGC 001039573 TGTGACCAG TGTGGAAT TCCTGCAGTGG AGTGGAAATTCCACAGCATGCCTGC SEC23A NM_006364 2133 CGTGTGCATT 2134 CCCATTACCA 2135 TCCTGGAGATGA 2136 CGTGTGCATTAGATCAGACAGGTCTCCTGGAGATGAAATGCTG AGATCAGACA TGTATCCTCC AATGCTGTCCCA TCCCAACCTTACTGGAGGATACATGGTAATGGG GG AG SEMA3A NM_006080 2137 TTGGAATGCA 2138 CTCTTCATTT 2139 TTGCCAATAGAC 2140 TTGGAATGCAGTCCGAAGTCGCAGAGAGCGCTGGTCTATTGG GTCCGAAGT CGCCTCTGGA CAGCGCTCTCTG CAATTCCAGAGGCGAAATGAAGAG SEPT9 NM_006640 2141 CAGTGACCAC 2142 CTTCGATGGT 2143 TTGCCAATAGAC 2144 CAGTGACCACGAGTACCAGGTCAACGGCAAGAGGATCCTTGG GAGTACCAGG ACCCCACTTG CAGCGCTCTCTG GAGGAAGACCAAGTGGGGTACCATCGAAG SERPINA3 NM_001085 2145 GTGTGGCCCT 2146 CCCTGTGCAT 2147 AGGGAATCGCTG 2148 GTGTGGCCCTGTCTGCTTATCCTTGGAAGGTGACAGCGATTCC GTCTGCTTA GTGAGAGCTA TCACCTTCCAAG CTGTGTAGCTCTCACATGCACAGGG C SERPINB5 NM_002639 2149 CAGATGGCCA 2150 GGCAGCATTA 2151 AGCTGACAACAG 2152 CAGATGGCCACTTTGAGAACATTTTAGCTGACAACAGTGTGAA CTTTGAGAAC ACCACAAGGA TGTGAACGACCA CGACCAGACCAAAATCCTTGTGGTTAATGCTGCC ATT TT GACC SESN3 NM_144665 2153 GACCCTGGTT 2154 GAGCTCGGAA 2155 TGCTCTTCTCCT 2156 GACCCTGGTTTTGGGTATGAAGACTTTGCCAGACGAGGAGAA TTGGGTATGA TGTTGGCA CGTCTGGCAAAG GAGCATTTGCCAACATTCCGAGCTC SFRP4 NM_003014 2157 TACAGGATGA 2158 GTTGTTAGGG 2159 CCTGGGACAGCC 2160 TACAGGATGAGGCTGGGCATTGCCTGGGACAGCCTATGTAAG GGCTGGGC CAAGGGGC TATGTAAGGCCA GCCATGTGCCCCTTGCCCTAACAAC SH3RF2 NM_152550 2161 CCATCACAAC 2162 CACTGGGGTG 2163 AACCGGATGGTC 2164 CCATCACAACAGCCTTGAACACTCTCAACCGGATGGTCCATTC AGCCTTGAAC CTGATCTCTA CATTCTCCTTCA TCCTTCAGGGCGCCATATGGTAGAGATCAGCACCCCAGTG SH3YL1 NM_015677 2165 CCTCCAAAGC 2166 CTTTGAGAGC 2167 CACAGCAGTCAT 2168 CCTCCAAAGCCATTGTCAAGACCACAGCAGTCATCTGCACCAG CATTGTCAAG CAGAGTTCAG CTGCACCAGTCC TCCAGCTGAACTCTGGCTCTCAAAG C SHH NM_000193 2169 GTCCAAGGCA 2170 GAAGCAGCCT 2171 CACCGAGTTCTC 2172 GTCCAAGGCACATATCCACTGCTCGGTGAAAGCAGAGAACTC CATATCCACT CCCGATTT TGCTTTCACCGA GGTGGCGGCCAAATCGGGAGGCTGCTTC G SHMT2 NM_005412 2173 AGCGGGTGCT 2174 ATGGCACTTC 2175 CCATCACTGCCA 2176 AGCGGGTGCTAGAGCTTGTATCCATCACTGCCAACAAGAACAC AGAGCTTGTA GGTCTCCA ACAAGAACACCT CTGTCCTGGAGACCGAAGTGCCAT G SIM2 NM_005069 2177 GATGGTAGGA 2178 CACAAGGAGC 2179 CGCCTCTCCACG 2180 GATGGTAGGAAGGGATGTGCCCGCCTCTCCACGCACTCAGCT AGGGATGTGC TGTGAATGAG CACTCAGCTAT ATACCTCATTCACAGCTCCTTGTG G SIPA1L1 NM_015556 2181 CTAGGACAGC 2182 CATAACCGTA 2183 CGCCACAATGCC 2184 CTAGGACAGCTTGGCTTCCATGTCAACTATGAGGGCATTGTGG TTGGCTTCCA GGGCTCCACA CTCATAGTTGAC CGGATGTGGAGCCCTACGGTTATG SKIL NM_005414 2185 AGAGGCTGAA 2186 CTATCGGCCT 2187 CCAATCTCTGCC 2188 AGAGGCTGAATATGCAGGACAGTTGGCAGAACTGAGGCAGAG TATGCAGGAC CAGCATGG TCAGTTCTGCCA ATTGGACCATGCTGAGGCCGATAG A SLC22A3 NM_021977 2189 ATCGTCAGCG 2190 CAGGATGGCT 2191 CAGCATCCACGC 2192 ATCGTCAGCGAGTTTGACCTTGTCTGTGTCAATGCGTGGATGC AGTTTGACCT TGGGTGAG ATTGACACAGAC TGGACCTCACCCAAGCCATCCTG SLC25A21 NM_030631 2193 AAGTGTTTTT 2194 GGCCGATCGA 2195 TCATGGTGCTGC 2196 AAGTGTTTTTCCCCCTTGAGATAATGGATATTTGCTATGCAGC CCCCCTTGAG TAGTCTCTCT ATAGCAAATATC ACCATGAAGAAGAGAGACTATCGATCGGCC AT T CA SLC44A1 NM_080546 2197 AGGACCGTAG 2198 ATCCCATCCC 2199 TACCATGGCTGC 2200 AGGACCGTAGCTGCACAGACATACCATGGCTGCTGCTCTTCAT CTGCACAGAC AATGCAGA TGCTCTTCATCC CCTCTTCTGCATTGGGATGGGAT SMAD4 NM_005359 2201 GGACATTACT 2202 ACCAATACTC 2203 TGCATTCCAGCC 2204 GGACATTACTGGCCTGTTCACAATGAGCTTGCATTCCAGCCTC GGCCTGTTCA AGGAGCAGGA TCCCATTTCCA CCATTTCCAATCATCCTGCTCCTGAGTATTGGT CA TGA SMARCC2 NM_003075 2205 TACCGACTGA 2206 GACATCACCC 2207 TATCTTACCTCT 2208 TACCGACTGAACCCCCAAGAGTATCTTACCTCTACCGCCTGCC ACCCCCAA GCTAGGTTTC ACCGCCTGCCGC GCCGAAACCTAGCGGGTGATGTC SMARCD1 NM_003076 2209 CCGAGTTAGC 2210 CCTTTGTGCC 2211 CCCACCCTTGCT 2212 CCGAGTTAGCATATCCCAGGCTCGCAGACTCAACACAGCAAG ATATCCCAGG CAGCTGTC GTGTTGAGTCTG GGTGGGAGACAGCTGGGCACAAAGG SMO NM_005631 2213 GGCATCCAGT 2214 CGCGATGTAG 2215 CTTCACAGAGGC 2216 GGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCAC GCCAGAAC CTGTGCAT TGAGCACCAGGA CAGGACATGCACAGCTACATCGCG SNAI1 NM_005985 2217 CCCAATCGGA 2218 GTAGGGCTGC 2219 TCTGGATTAGAG 2220 CCCAATCGGAAGCCTAACTACAGCGAGCTGCAGGACTCTAAT AGCCTAACTA TGGAAGGTAA TCCTGCAGCTCG CCAGAGTTTACCTTCCAGCAGCCCTAC C SNRPB2 NM_003092 2221 CGTTTCCTGC 2222 AGGTAGAAGG 2223 CCCACCTAAGGC 2224 CGTTTCCTGCTTTTGGTTCTTACAGTAGTCGGCGTAGGCCTTA TTTTGGTTCT CGCACGAA CTACGCCGACTA GGTGGGTTCGTGCGCCTTCTACCT SOD1 NM_000454 2225 TGAAGAGAGG 2226 AATAGACACA 2227 TTTGTCAGCAGT 2228 TGAAGAGAGGCATGTTGGAGACTTGGGCAATGTGACTGCTGA CATGTTGGAG TCGGCCACAC CACATTGCCCAA CAAAGATGGTGTGGCCGATGTGTCTATT SORBS1 NM_015385 2229 GCAGATGAGT 2230 AGCGAGTGAA 2231 ATTTCCATTGGC 2232 GCAGATGAGTGGAGGCTTTCTTCCAGTGCTGATGCCAATGGAA GGAGGCTTTC GAGGGCTG ATCAGCACTGGA ATGCCCAGCCCTCTTCACTCGCT SOX4 NM_003107 2233 AGATGATCTC 2234 GCGCCCTTCA 2235 CGAGTCCAGCAT 2236 AGATGATCTCGGGAGACTGGCTCGAGTCCAGCATCTCCAACC GGGAGACTGG GTAGGTGA CTCCAACCTGGT TGGTTTTCACCTACTGAAGGGCGC SPARC NM_003118 2237 TCTTCCCTGT 2238 AGCTCGGTGT 2239 TGGACCAGCACC 2240 TCTTCCCTGTACACTGGCAGTTCGGCCAGCTGGACCAGCACC ACACTGGCAG GGGAGAGGTA CCATTGACGG CCATTGACGGGTACCTCTCCCACACCGAGCT TTC SPARCL1 NM_004684 2241 GGCACAGTGC 2242 GATTGAGCTC 2243 ACTTCATCCCAA 2244 GGCACAGTGCAAGTGATGACTACTTCATCCCAAGCCAGGCCTT AAGTGATGA TCTCGGCCT GCCAGGCCTTTC TCTGGAGGCCGAGAGAGCTCAATC SPDEF NM_012391 2245 CCATCCGCCA 2246 GGGTGCACGA 2247 ATCATCCGGAAG 2248 CCATCCGCCAGTATTACAAGAAGGGCATCATCCGGAAGCCAG GTATTACAAG ACTGGTAGA CCAGACATCTCC ACATCTCCCAGCGCCTCGTCTACCAGTTCGTGCACCC SPINK1 NM_003122 2249 CTGCCATATG 2250 GTTGAAAACT 2251 ACCACGTCTCTT 2252 CTGCCATATGACCCTTCCAGTCCCAGGCTTCTGAAGAGACGTG ACCCTTCCAG GCACCGCAC CAGAAGCCTGGG GTAAGTGCGGTGCAGTTTTCAAC SPINT1 NM_003710 2253 ATTCCCAGCA 2254 AGATGGCTAC 2255 CTGTCGCAGTGT 2256 ATTCCCAGCACAGGCTCTGTGGAGATGGCTGTCGCAGTGTTC CAGGCTCTGT CACCACCACA TCCTGGTCATCT CTGGTCATCTGCATTGTGGTGGTGGTAGCCATCT A GC SPP1 NM_ 2257 TCACACATGG 2258 GTTCAGGTCC 2259 TGAATGGTGCAT 2260 TCACACATGGAAAGCGAGGAGTTGAATGGTGCATACAAGGCC 001040058 AAAGCGAGG TGGGCAAC ACAAGGCCATCC ATCCCCGTTGCCCAGGACCTGAAC SOLE NM_003129 2261 ATTTTCGAGG 2262 CCTGAGCAAG 2263 TGGGCAAGAAAA 2264 ATTTTCGAGGCCAAAAAATCATTTTACTGGGCAAGAAAAACAT CCAAAAAATC GATATTCACG ACATCTCATTCC CTCATTCCTTTGTCGTGAATATCCTTGCTCAGG TTTG SRC NM_005417 2265 TGAGGAGTGG 2266 CTCTCGGGTT 2267 AACCGCTCTGAC 2268 TGAGGAGTGGTATTTTGGCAAGATCACCAGACGGGAGTCAGA TATTTTGGCA CTCTGCATTG TCCCGTCTGGTG GCGGTTACTGCTCAATGCAGAGAACCCGAGAG AGA A SRD5A1 NM_001047 2269 GGGCTGGAAT 2270 CCATGACTGC 2271 CCTCTCTCGGAG 2272 GGGCTGGAATCTGTCTAGGAGCCCTCTCTCGGAGGCCACAGA CTGTCTAGGA ACAATGGCT GCCACAGAGGCT GGCTGGGGGTAGCCATTGTGCAGTCATGG SRD5A2 NM_000348 2273 GTAGGTCTCC 2274 TCCCTGGAAG 2275 AGACACCACTCA 2276 GTAGGTCTCCTGGCGTTCTGCCAGCTGGCCTGGGGATTCTGA TGGCGTTCTG GGTAGGAGTA GAATCCCCAGGC GTGGTGTCTGCTTAGAGTTTACTCCTACCCTTCCAGGGA A ST5 NM_005418 2277 CCTGTCCTGC 2278 CAGCTGCACA 2279 AGTCACGAGCAC 2280 CCTGTCCTGCCAGAGCATGGATGAAGTTTCGCTGGGTGCTCGT CAGAGCAT AAACTGGC CCAGCGAAACTT GACTGGCCAGTTTTGTGCAGCTG STAT1 NM_007315 2281 GGGCTCAGCT 2282 ACATGTTCAG 2283 TGGCAGTTTTCT 2284 GGGCTCAGCTTTCAGAAGTGCTGAGTTGGCAGTTTTCTTCTGT TTCAGAAGTG CTGGTCCACA TCTGTCACCAAA CACCAAAAGAGGTCTCAATGTGGACCAGCTGAACATGT A STAT3 NM_003150 2285 TCACATGCCA 2286 CTTGCAGGAA 2287 TCCTGGGAGAGA 2288 TCACATGCCACTTTGGTGTTTCATAATCTCCTGGGAGAGATTG CTTTGGTGTT GCGGCTATAC TTGACCAGCA ACCAGCAGTATAGCCGCTTCCTGCAAG STAT5A NM_003152 2289 GAGGCGCTCA 2290 GCCAGGAACA 2291 CGGTTGCTCTGC 2292 GAGGCGCTCAACATGAAATTCAAGGCCGAAGTGCAGAGCAAC ACATGAAATT CGAGGTTCTC ACTTCGGCCT CGGGGCCTGACCAAGGAGAACCTCGTGTTCCTGGC C STAT5B NM_012448 2293 CCAGTGGTGG 2294 GCAAAAGCAT 2295 CAGCCAGGACAA 2296 CCAGTGGTGGTGATCGTTCATGGCAGCCAGGACAACAATGCG TGATCGTTCA TGTCCCAGAG CAATGCGACGG ACGGCCACTGTTCTCTGGGACAATGCTTTTGC A STMN1 NM_005563 2297 AATACCCAAC 2298 GGAGACAATG 2299 CACGTTCTCTGC 2300 AATACCCAACGCACAAATGACCGCACGTTCTCTGCCCCGTTTC GCACAAATGA CAAACCACAC CCCGTTTCTTG TTGCCCCAGTGTGGTTTGCATTGTCTCC STS NM_000351 2301 GAAGATCCCT 2302 GGATGATGTT 2303 CTGCGTGGCTCT 2304 GAAGATCCCTTTCCTCCTACTGTTCTTTCTGTGGGAAGCCGAG TTCCTCCTAC CGGCCTTGAT CGGCTTCCCA AGCCACGCAGCATCAAGGCCGAACATCATCC TGTTC SULF1 NM_015170 2305 TGCAGTTGTA 2306 TCTCAAGAAT 2307 TACCGTGCCAGC 2308 TGCAGTTGTAGGGAGTCTGGTTACCGTGCCAGCAGAAGCCAA GGGAGTCTGG TGCCGTTGAC AGAAGCCAAAG AGAAAGAGTCAACGGCAATTCTTGAGA SUMO1 NM_003352 2309 GTGAAGCCAC 2310 CCTTCCTTCT 2311 CTGACCAGGAGG 2312 GTGAAGCCACCGTCATCATGTCTGACCAGGAGGCAAAACCTTC CGTCATCATG TATCCCCCAA CAAAACCTTCAA AACTGAGGACTTGGGGGATAAGAAGGAAGG GT CTGA SVIL NM_003174 2313 ACTTGCCCAG 2314 GACACCATCC 2315 ACCCCAGGACTG 2316 ACTTGCCCAGCACAAGGAAGACCCCAGGACTGATGTCAAGGC CACAAGGA GTGTCACATC ATGTCAAGGCAT ATACGATGTGACACGGATGGTGTC TAF2 NM_003184 2317 GCGCTCCACT 2318 CTTGTGCTCA 2319 AGCCTCCAAACA 2320 GCGCTCCACTCTCAGTCTTTACTAAGGAATCTACAGCCTCCAA CTCAGTCTTT TGGTGATGGT CAGTGACCACCA ACACAGTGACCACCATCACCACCATCACCATGAGCACAAG TARP NM_ 2321 GAGCAACACG 2322 GGCACCGTTA 2323 TCTTCATGGTGT 2324 GAGCAACACGATTCTGGGATCCCAGGAGGGGAACACCATGAA 001003799 ATTCTGGGA ACCAGCTAAA TCCCCTCCTGG GACTAACGACACATACATGAAATTTAGCTGGTTAACGGTGCC T TBP NM_003194 2325 GCCCGAAACG 2326 CGTGGCTCTC 2327 TACCGCAGCAAA 2328 GCCCGAAACGCCGAATATAATCCCAAGCGGTTTGCTGCGGTA CCGAATATA TTATCCTCAT CCGCTTGGG ATCATGAGGATAAGAGAGCCACG GAT TFDP1 NM_007111 2329 TGCGAAGTGC 2330 GCCTTCCAGA 2331 CGCACCAGCATG 2332 TGCGAAGTGCTTTTGTTTGTTTGTTTTCGTTTGGTTAAAGCTT TTTTGTTTGT CAGTCTCCAT GCAATAAGCTTT ATTGCCATGCTGGTGCGGCTATGGAGACTGTCTGGAAGGC TFF1 NM_003225 2333 GCCCTCCCAG 2334 CGTCGATGGT 2335 TGCTGTTTCGAC 2336 GCCCTCCCAGTGTGCAAATAAGGGCTGCTGTTTCGACGACAC TGTGCAAAT ATTAGGATAG GACACCGTTCG CGTTCGTGGGGTCCCCTGGTGCTTCTATCCTAATACCATCGAC AAGCA G TFF3 NM_003226 2337 AGGCACTGTT 2338 CATCAGGCTC 2339 CAGAAGCGCTTG 2340 AGGCACTGTTCATCTCAGCTTTTCTGTCCCTTTGCTCCCGGCA CATCTCAGTT CAGATATGAA CCGGGAGCAAAG AGCGCTTCTGCTGAAAGTTCATATCTGGAGCCTGATG TTTCT CTTTC G TGFA NM_003236 2341 GGTGTGCCAC 2342 ACGGAGTTCT 2343 TTGGCCTGTAAT 2344 GGTGTGCCACAGACCTTCCTACTTGGCCTGTAATCACCTGTGC AGACCTTCCT TGACAGAGTT CACCTGTGCAGC AGCCTTTTGTGGGCCTTCAAAACTCTGTCAAGAACTCCGT TTGA CTT TGFB1I1 NM_ 2345 GCTACTTTGA 2346 GGTCACCATC 2347 CAAGATGTGGCT 2348 GCTACTTTGAGCGCTTCTCGCCAAGATGTGGCTTCTGCAACCA 001042454 GCGCTTCTCG TTGTGTCGG TCTGCAACCAGC GCCCATCCGACACAAGATGGTGACC TGFB2 NM_003238 2349 ACCAGTCCCC 2350 CCTGGTGCTG 2351 TCCTGAGCCCGA 2352 ACCAGTCCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCC CAGAAGACTA TTGTAGATGG GGAAGTCCC CCGGAGGTGATTTCCATCTACAACAGCACCAGG TGFB3 NM_003239 2353 GGATCGAGCT 2354 GCCACCGATA 2355 CGGCCAGATGAG 2356 GGATCGAGCTCTTCCAGATCCTTCGGCCAGATGAGCACATTGC CTTCCAGATC TAGCGCTGTT CACATTGCC CAAACAGCGCTATATCGGTGGC CT TGFBR2 NM_003242 2357 AACACCAATG 2358 CCTCTTCATC 2359 TTCTGGGCTCCT 2360 AACACCAATGGGTTCCATCTTTCTGGGCTCCTGATTGCTCAAG GGTTCCATCT AGGCCAAACT GATTGCTCAAGC CACAGTTTGGCCTGATGAAGAGG THBS2 NM_003247 2361 CAAGACTGGC 2362 CAGCGTAGGT 2363 TGAGTCTGCCAT 2364 CAAGACTGGCTACATCAGAGTCTTAGTGCATGAAGGAAAACAG TACATCAGAG TTGGTCATAG GACCTGTTTTCC GTCATGGCAGACTCAGGACCTATCTATGACCAAACCTACGCTG TCTTAGTG ATAGG TTCAT THY1 NM_006288 2365 GGACAAGACC 2366 TTGGAGGCTG 2367 CAAGCTCCCAAG 2368 GGACAAGACCCTCTCAGGCTGTCCCAAGCTCCCAAGAGCTTC CTCTCAGGCT TGGGTCAG AGCTTCCAGAGC CAGAGCTCTGACCCACAGCCTCCAA TIAM1 NM_003253 2369 GTCCCTGGCT 2370 GGGCTCCCGA 2371 TGGAGCCCTTCT 2372 GTCCCTGGCTGAAAATGGCCTGGAGCCCTTCTCCCAAGATGG GAAAATGG AGTCTTCTA CCCAAGATGGTA TACCCTAGAAGACTTCGGGAGCCC TIMP2 NM_003255 2373 TCACCCTCTG 2374 TGTGGTTCAG 2375 CCCTGGGACACC 2376 TCACCCTCTGTGACTTCATCGTGCCCTGGGACACCCTGAGCAC TGACTTCATC GCTCTTCTTC CTGAGCACCA CACCCAGAAGAAGAGCCTGAACCACA GT TG TIMP3 NM_000362 2377 CTACCTGCCT 2378 ACCGAAATTG 2379 CCAAGAACGAGT 2380 CTACCTGCCTTGCTTTGTGACTTCCAAGAACGAGTGTCTCTGG TGCTTTGTGA GAGAGCATGT GTCTCTGGACCG ACCGACATGCTCTCCAATTTCGGT TK1 NM_003258 2381 GCCGGGAAGA 2382 CAGCGGCACC 2383 CAAATGGCTTCC 2384 GCCGGGAAGACCGTAATTGTGGCTGCACTGGATGGGACCTTC CCGTAATTGT AGGTTCAG TCTGGAAGGTCC CAGAGGAAGCCATTTGGGGCCATCCTGAACCTGGTGCCGCTG CA TMPRSS2 NM_005656 2385 GGACAGTGTG 2386 CTCCCACGAG 2387 AAGCACTGTGCA 2388 GGACAGTGTGCACCTCAAAGACTAAGAAAGCACTGTGCATCAC CACCTCAAAG GAAGGTCC TCACCTTGACCC CTTGACCCTGGGGACCTTCCTCGTGGGAG TMPRSS2 DQ204772 2389 GAGGCGGAGG 2390 ACTGGTCCTC 2391 TAAGGCTTCCTG 2392 GAGGCGGAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTG ERG A GCGAG ACTCACAACT CCGCGCTCCA GAGCGCGGCAGGAAGCCTTATCAGTTGTGAGTGAGGACCAGT TMPRSS2 DQ204773 2393 GAGGCGGAGG 2394 TTCCTCGGGT 2395 CCTGGAATAACC 2396 GAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTGGAGCGC ERG B GCGAG CTCCAAAGAT TGCCGCGC GGCAGGTTATTCCAGGATCTTTGGAGACCCGAGGAA TNF NM_000594 2397 GGAGAAGGGT 2398 TGCCCAGACT 2399 CGCTGAGATCAA 2400 GGAGAAGGGTGACCGACTCAGCGCTGAGATCAATCGGCCCGA GACCGACTCA CGGCAAAG TCGGCCCGACTA CTATCTCGACTTTGCCGAGTCTGGGCA TNFRS NM_003844 2401 TGCACAGAGG 2402 TCTTCATCTG 2403 CAATGCTTCCAA 2404 TGCACAGAGGGTGTGGGTTACACCAATGCTTCCAACAATTTGT F10A GTGTGGGTTA ATTTACAAGC CAATTTGTTTGC TTGCTTGCCTCCCATGTACAGCTTGTAAATCAGATGAAGA C TGTACATG TTGCC TNFRS NM_003842 2405 CTCTGAGACA 2406 CCATGAGGCC 2407 CAGACTTGGTGC 2408 CTCTGAGACAGTGCTTCGATGACTTTGCAGACTTGGTGCCCTT F10B GTGCTTCGAT CAACTTCCT CCTTTGACTCC TGACTCCTGGGAGCCGCTCATGAGGAAGTTGGGCCTCATGG GACT TNFRSF18 NM_148901 2409 CAGAAGCTGC 2410 CACCCACAGG 2411 CCTTCTCCTCTG 2412 CAGAAGCTGCCAGTTCCCCGAGGAAGAGCGGGGCGAGCGAT CAGTTCCC TCTCCCAG CCGATCGCTC CGGCAGAGGAGAAGGGGCGGCTGGGAGACCTGTGGGTG TNFSF10 NM_003810 2413 CTTCACAGTG 2414 CATCTGCTTC 2415 AAGTACACGTAA 2416 CTTCACAGTGCTCCTGCAGTCTCTCTGTGTGGCTGTAACTTAC CTCCTGCAGT AGCTCGTTGG GTTACAGCCACA GTGTACTTTACCAACGAGCTGAAGCAGATG CT T CA TNFSF11 NM_003701 2417 AACTGCATGT 2418 TGACACCCTC 2419 ACATGACCAGGG 2420 AACTGCATGTGGGCTATGGGAGGGGTTGGTCCCTGGTCATGT GGGCTATGG TCCACTTCAG ACCAACCCCTC GCCCCTTCGCAGCTGAAGTGGAGAGGGTGTCA TOP2A NM_001067 2421 AATCCAAGGG 2422 GTACAGATTT 2423 CATATGGACTTT 2424 AATCCAAGGGGGAGAGTGATGACTTCCATATGGACTTTGACTC GGAGAGTGAT TGCCCGAGGA GACTCAGCTGTG AGCTGTGGCTCCTCGGGCAAAATCTGTAC GC TP53 NM_000546 2425 CTTTGAACCC 2426 CCCGGGACAA 2427 AAGTCCTGGGTG 2428 CTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGCACCCA TTGCTTGCAA AGCAAATG CTTCTGACGCAC GGACTTCCATTTGCTTTGTCCCGGG A TP63 NM_003722 2429 CCCCAAGCAG 2430 GAATCGCACA 2431 CCCGGGTCTCAC 2432 CCCCAAGCAGTGCCTCTACAGTCAGTGTGGGCTCCAGTGAGA TGCCTCTACA GCATCAATAA TGGAGCCCA CCCGGGGTGAGCGTGTTATTGATGCTGTGCGATTC CAC TPD52 NM_005079 2433 GCCTGTGAGA 2434 ATGTGCTTGG 2435 TCTGCTACCCAC 2436 GCCTGTGAGATTCCTACCTTTGTTCTGCTACCCACTGCCAGAT TTCCTACCTT ACCTCGCTT TGCCAGATGCTG GCTGCAAGCGAGGTCCAAGCACAT TG TPM1 NM_ 2437 TCTCTGAGCT 2438 GGCTCTAAGG 2439 TTCTCCAGCTGA 2440 TCTCTGAGCTCTGCATTTGTCTATTCTCCAGCTGACCCTGGTT 001018005 CTGCATTTGT CAGGATGCTA CCCTGGTTCTCT CTCTCTCTTAGCATCCTGCCTTAGAGCC C C TPM2 NM_213674 2441 AGGAGATGCA 2442 CCACCTCTTC 2443 CCAAGCACATCG 2444 AGGAGATGCAGCTGAAGGAGGCCAAGCACATCGCTGAGGATT GCTGAAGGAG ATATTTGCGG CTGAGGATTCAG CAGACCGCAAATATGAAGAGGTGG TPP2 NM_003291 2445 TAACCGTGGC 2446 ATGCCAACGC 2447 ATCCTGTTCAGG 2448 TAACCGTGGCATCTACCTCCGAGATCCTGTTCAGGTGGCTGCA ATCTACCTCC CATGATCT TGGCTGCACCTT CCTTCAGATCATGGCGTTGGCAT TPX2 NM_012112 2449 TCAGCTGTGA 2450 ACGGTCCTAG 2451 CAGGTCCCATTG 2452 TCAGCTGTGAGCTGCGGATACCGCCCGGCAATGGGACCTGCT GCTGCGGATA GTTTGAGGTT CCGGGCG CTTAACCTCAAACCTAGGACCGT AAGA TRA2A NM_013293 2453 GCAAATCCAG 2454 CTTCACGAAG 2455 AACTGAGGCCAA 2456 GCAAATCCAGATCCCAACACTTGCCTTGGAGTGTTTGGCCTCA ATCCCAACAC ATCCCTCTCT ACACTCCAAGGC GTTTGTACACAACAGAGAGGGATCTTCGTGAAG G TRAF3IP2 NM_147200 2457 CCTCACAGGA 2458 CTGGGGCTGG 2459 TGGATCTGCCAA 2460 CCTCACAGGAACCGAGCAGGCCTGGATCTGCCAACCATAGAC ACCGAGCA GAATCATA CCATAGACACGG ACGGGATATGATTCCCAGCCCCAG TRAM1 NM_014294 2461 CAAGAAAAGC 2462 ATGTCCGCGT 2463 AGTGCTGAGCCA 2464 CAAGAAAAGCACCAAGAGCCCCCCAGTGCTGAGCCACGAATT ACCAAGAGCC GATTCTGC CGAATTCGTCC CGTCCTGCAGAATCACGCGGACAT TRAP1 NM_016292 2465 TTACCAGTGG 2466 TGTCCCGGTT 2467 TTCGGCGATTTC 2468 TTACCAGTGGCTTTCAGATGGTTCTGGAGTGTTTGAAATCGCC CTTTCAGATG CTAACTCCC AAACACTCCAGA GAAGCTTCGGGAGTTAGAACCGGGACA G TRIM14 NM_033220 2469 CATTCGCCTT 2470 CAAGGTACCT 2471 AACTGCCAGCTC 2472 CATTCGCCTTAAGGAAAGCATAAACTGCCAGCTCTCAGACCCT AAGGAAAGCA GGCTTGGTG TCAGACCCTTCC TCCAGCACCAAGCCAGGTACCTTG TRO NM_177556 2473 GCAACTGCCA 2474 TGGTGTGGAT 2475 CCACCCAAGGCC 2476 GCAACTGCCACCCATACAGCTACCACCCAAGGCCAAATTACCA CCCATACAG ACTGGCTGTC AAATTACCAATG ATGAGACAGCCAGTATCCACACCA TRPC6 NM_004621 2477 CGAGAGCCAG 2478 TAGCCGTAGC 2479 CTTCTCCCAGCT 2480 CGAGAGCCAGGACTATCTGCTCATGGACTCGGAGCTGGGAGA GACTATCTGC AAGGCAGC CCGAGTCCATG AGACGGCTGCCCGCAAGCCCCGCTGCCTTGCTACGGCTA TRPV6 NM_018646 2481 CCGTAGTCCC 2482 TCCTCACTGT 2483 ACTTTGGGGAGC 2484 CCGTAGTCCCTGCAACCTCATCTACTTTGGGGAGCACCCTTTG TGCAACCTC TCACACAGGC ACCCTTTGTCCT TCCTTTGCTGCCTGTGTGAACAGTGAGGA TSTA3 NM_003313 2485 CAATTTGGAC 2486 CACCTCAAAG 2487 AACGTGCACATG 2488 CAATTTGGACTTCTGGAGGAAAAACGTGCACATGAACGACAAC TTCTGGAGGA GCCGAGTG AACGACAACGTC GTCCTGCACTCGGCCTTTGAGGTG A TUBB2A NM_001069 2489 CGAGGACGAG 2490 ACCATGCTTG 2491 TCTCAGATCAAT 2492 CGAGGACGAGGCTTAAAAACTTCTCAGATCAATCGTGCATCCT GCTTAAAAAC AGGACAACAG CGTGCATCCTTA TAGTGAACTTCTGTTGTCCTCAAGCATGGT GTGAA TYMP NM_001953 2493 CTATATGCAG 2494 CCACGAGTTT 2495 ACAGCCTGCCAC 2496 CTATATGCAGCCAGAGATGTGACAGCCACCGTGGACAGCCTG CCAGAGATGT CTTACTGAGA TCATCACAGCC CCACTCATCACAGCCTCCATTCTCAGTAAGAAACTCGTGG GACA ATGG TYMS NM_001071 2497 GCCTCGGTGT 2498 CGTGATGTGC 2499 CATCGCCAGCTA 2500 GCCTCGGTGTGCCTTTCAACATCGCCAGCTACGCCCTGCTCAC GCCTTTCA GCAATCATG CGCCCTGCTC GTACATGATTGCGCACATCACG UAP1 NM_003115 2501 CTGGAGACGG 2502 GCCAAGCTTT 2503 TACCTGTAAACC 2504 CTGGAGACGGTCGTAGCTGCGGTCGCGCCGAGAAAGGTTTAC TCGTAGCTG GTAGAAATAG TTTCTCGGCGCG AGGTACATACATTACACCCCTATTTCTACAAAGCTTGGC GG UBE2C NM_007019 2505 TGTCTGGCGA 2506 ATGGTCCCTA 2507 TCTGCCTTCCCT 2508 TGTCTGGCGATAAAGGGATTTCTGCCTTCCCTGAATCAGACAA TAAAGGGATT CCCATTTGAA GAATCAGACAAC CCTTTTCAAATGGGTAGGGACCAT C UBE2G1 NM_003342 2509 TGACACTGAA 2510 AAGCAGAGAG 2511 TTGTCCCACCAG 2512 TGACACTGAACGAGGTGGCTTTTGTCCCACCAGTGCCTCATCA CGAGGTGGC GAATCGCCT TGCCTCATCAGT GTGTGAGGCGATTCCTCTCTGCTT UBE2T NM_014176 2513 TGTTCTCAAA 2514 AGAGGTCAAC 2515 AGGTGCTTGGAG 2516 TGTTCTCAAATTGCCACCAAAAGGTGCTTGGAGACCATCCCTC TTGCCACCAA ACAGTTGCGA ACCATCCCTCAA AACATCGCAACTGTGTTGACCTCT UGDH NM_003359 2517 GAAACTCCAG 2518 CTCTGGGAAC 2519 TATACAGCACAC 2520 GAAACTCCAGAGGGCCAGAGAGCTGTGCAGGCCCTGTGTGCT AGGGCCAGA CCAGTGCTC AGGGCCTGCACA GTATATGAGCACTGGGTTCCCAGAG UGT2B15 NM_001076 2521 AAGCCTGAAG 2522 CCTCCATTTA 2523 AAAGATGGGACT 2524 AAGCCTGAAGTGGAATGACTGAAAGATGGGACTCCTCCTTTAT TGGAATGACT AAACCCTCCA CCTCCTTTATTT TTCAGCATGGAGGGTTTTAAATGGAGG G CAGCA UGT2B17 NM_001077 2525 TTGAGTTTGT 2526 TCCAGGTGAG 2527 ACCCGAAGGTGC 2528 TTGAGTTTGTCATGCGCCATAAAGGAGCCAAGCACCTTCGGGT CATGCGCC GTTGTGGG TTGGCTCCTTTA CGCAGCCCACAACCTCACCTGGA UHRF1 NM_013282 2529 CTACAGGGGC 2530 GGTGTCATTC 2531 CGGCCATACCCT 2532 CTACAGGGGCAAACAGATGGAGGACGGCCATACCCTCTTCGA AAACAGATGG AGGCGGAC CTTCGACTACGA CTACGAGGTCCGCCTGAATGACACC UTP23 NM_032334 2533 GATTGCACAA 2534 GGAAAGCAGA 2535 TCGAAATTGTCC 2536 GATTGCACAAAAATGCCAAGTTCGAAATTGTCCTCATTTCAAG AAATGCCAAG CATTCTGATC TCATTTCAAGAA AATGCAGTGAGTGGATCAGAATGTCTGCTTTCC C TGCA VCAM1 NM_001078 2537 TGGCTTCAGG 2538 TGCTGTCGTG 2539 CAGGCACACACA 2540 TGGCTTCAGGAGCTGAATACCCTCCCAGGCACACACAGGTGG AGCTGAATAC ATGAGAAAAT GGTGGGACACAA GACACAAATAAGGGTTTTGGAACCACTATTTTCTCATCACGAC C AGTG AT AGCA VCL NM_003373 2541 GATACCACAA 2542 TCCCTGTTAG 2543 AGTGGCAGCCAC 2544 GATACCACAACTCCCATCAAGCTGTTGGCAGTGGCAGCCACG CTCCCATCAA GCGCATCAG GGCGCC GCGCCTCCTGATGCGCCTAACAGGGA GCT VCPIP1 NM_025054 2545 TTTCTCCCAG 2546 TGAATAGGGA 2547 TGGTCCATCCTC 2548 TTTCTCCCAGTACCATTCGTGATGGTCCATCCTCTGCACCTGC TACCATTCGT GCCTTGGTAG TGCACCTGCTAC TACACCTACCAAGGCTCCCTATTCA G G VDR NM_000376 2549 CCTCTCCTTC 2550 TCATTGCCAA 2551 CAGCATGAAGCT 2552 CCTCTCCTTCCAGCCTGAGTGCAGCATGAAGCTAACGCCCCTT CAGCCTGAGT ACACTTCGAG AACGCCCCTTGT GTGCTCGAAGTGTTTGGCAATGA VEGFA NM_003376 2553 CTGCTGTCTT 2554 GCAGCCTGGG 2555 TTGCCTTGCTGC 2556 CTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCTCTACC GGGTGCATTG ACCACTTG TCTACCTCCACC TCCACCATGCCAAGTGGTCCCAGGCTGC A VEGFB NM_003377 2557 TGACGATGGC 2558 GGTACCGGAT 2559 CTGGGCAGCACC 2560 TGACGATGGCCTGGAGTGTGTGCCCACTGGGCAGCACCAAGT CTGGAGTGT CATGAGGATC AAGTCCGGA CCGGATGCAGATCCTCATGATCCGGTACC TG VEGFC NM_005429 2561 CCTCAGCAAG 2562 AAGTGTGATT 2563 CCTCTCTCTCAA 2564 CCTCAGCAAGACGTTATTTGAAATTACAGTGCCTCTCTCTCAA ACGTTATTTG GGCAAAACTG GGCCCCAAACCA GGCCCCAAACCAGTAACAATCAGTTTTGCCAATCACACTT AAATT ATTG GT VIM NM_003380 2565 TGCCCTTAAA 2566 GCTTCAACGG 2567 ATTTCACGCATC 2568 TGCCCTTAAAGGAACCAATGAGTCCCTGGAACGCCAGATGCG GGAACCAATG CAAAGTTCTC TGGCGTTCCA TGAAATGGAAGAGAACTTTGCCGTTGAAGC A TT VTI1B NM_006370 2569 ACGTTATGCA 2570 CCGATGGAGT 2571 CGAAACCCCATG 2572 ACGTTATGCACCCCTGTCTTTCCGAAACCCCATGATGTCTAAG CCCCTGTCTT TTAGCAAGGT ATGTCTAAGCTT CTTCGAAACTACCGGAAGGACCTTGCTAAACTCCATCGG CG WDR19 NM_025132 2573 GAGTGGCCCA 2574 GATGCTTGAG 2575 CCCCTCGACGTA 2576 GAGTGGCCCAGATGTCCATAAGAATGGGAGACATACGTCGAG GATGTCCATA GGCTTGGTT TGTCTCCCATTC GGGTTAACCAAGCCCTCAAGCATC WFDC1 NM_021197 2577 ACCCCTGCTC 2578 ATACCTTCGG 2579 CTATGAGTGCCA 2580 ACCCCTGCTCTGTCCCTCGGGCTATGAGTGCCACATCCTGAG TGTCCCTC CCACGTCAC CATCCTGAGCCC CCCAGGTGACGTGGCCGAAGGTAT WISP1 NM_003882 2581 AGAGGCATCC 2582 CAAACTCCAC 2583 CGGGCTGCATCA 2584 AGAGGCATCCATGAACTTCACACTTGCGGGCTGCATCAGCACA ATGAACTTCA AGTACTTGGG GCACACGC CGCTCCTATCAACCCAAGTACTGTGGAGTTTG CA TTGA WNT5A NM_003392 2585 GTATCAGGAC 2586 TGTCGGAATT 2587 TTGATGCCTGTC 2588 GTATCAGGACCACATGCAGTACATCGGAGAAGGCGCGAAGAC CACATGCAGT GATACTGGCA TTCGCGCCTTCT AGGCATCAAAGAATGCCAGTATCAATTCCGACA ACATC TT WWOX NM_016373 2589 ATCGCAGCTG 2590 AGCTCCCTGT 2591 CTGCTGTTTACC 2592 ATCGCAGCTGGTGGGTGTACACACTGCTGTTTACCTTGGCGAG GTGGGTGTAC TGCATGGACT TTGGCGAGGCCT GCCTTTCACCAAGTCCATGCAACAGGGAGCT T TTC XIAP NM_001167 2593 GCAGTTGGAA 2594 TGCGTGGCAC 2595 TCCCCAAATTGC 2596 GCAGTTGGAAGACACAGGAAAGTATCCCCAAATTGCAGATTTA GACACAGGAA TATTTTCAAG AGATTTATCAAC TCAACGGCTTTTATCTTGAAAATAGTGCCACGCA AGT A GGC XRCC5 NM_021141 2597 AGCCCACTTC 2598 AGCAGGATTC 2599 TCTGGCTGAAGG 2600 AGCCCACTTCAGCGTCTCCAGTCTGGCTGAAGGCAGTGTCAC AGCGTCTC ACACTTCCAA CAGTGTCACCTC CTCTGTTGGAAGTGTGAATCCTGCT C YY1 NM_003403 2601 ACCCGGGCAA 2602 GACCGAGAAC 2603 TTGATCTGCACC 2604 ACCCGGGCAACAAGAAGTGGGAGCAGAAGCAGGTGCAGATCA CAAGAAGT TCGCCCTC TGCTTCTGCTCC AGACCCTGGAGGGCGAGTTCTCGGTC ZFHX3 NM_006885 2605 CTGTGGAGCC 2606 GGAGCAGGGT 2607 ACCTGGCCCAAC 2608 CTGTGGAGCCTCTGCCTGCGGACCTGGCCCAACTCTACCAGC TCTGCCTG TGGATTGAG TCTACCAGCATC ATCAGCTCAATCCAACCCTGCTCC ZFP36 NM_003407 2609 CATTAACCCA 2610 CCCCCACCAT 2611 CAGGTCCCCAAG 2612 CATTAACCCACTCCCCTGACCTCACGCTGGGGCAGGTCCCCA CTCCCCTGA CATGAATACT TGTGCAAGCTC AGTGTGCAAGCTCAGTATTCATGATGGTGGGGG ZMYND8 NM_183047 2613 GGTCTGGGCC 2614 TGCCCGTCTT 2615 CTTTTGCAGGCC 2616 GGTCTGGGCCAAACTGAAGGGGTTTCCATTCTGGCCTGCAAAA AAACTGAAG TATCCCTTAG AGAATGGAAACC GCTCTAAGGGATAAAGACGGGCA ZNF3 NM_017715 2617 CGAAGGGACT 2618 GCAGGAGGTC 2619 AGGAGGTTCCAC 2620 CGAAGGGACTCTGCTCCAGTGAACTGGCGAGTGTGGAACCTC CTGCTCCA CTCAGAAGG ACTCGCCAGTTC CTGACACCTTCTGAGGACCTCCTGC ZNF827 NM_178835 2621 TGCCTGAGGA 2622 GAGGTGGCGG 2623 CCCGCCTTCAGA 2624 TGCCTGAGGACCCTCTACCGCCCCCGCCTTCAGAGAAGAAAC CCCTCTACC AGTGACTTT GAAGAAACCAGA CAGAAAAAGTCACTCCGCCACCTC ZWINT NM_007057 2625 TAGAGGCCAT 2626 TCCGTTTCCT 2627 ACCAAGGCCCTG 2628 TAGAGGCCATCAAAATTGGCCTCACCAAGGCCCTGACTCAGAT CAAAATTGGC CTGGGCTT ACTCAGATGGAG GGAGGAAGCCCAGAGGAAACGGA

TABLE B SEQ ID microRNA Sequence NO hsa-miR-1 UGGAAUGUAAAGAAGUAUGUAU 2629 hsa-miR-103 GCAGCAUUGUACAGGGCUAUGA 2630 hsa-miR-106b UAAAGUGCUGACAGUGCAGAU 2631 hsa-miR-10a UACCCUGUAGAUCCGAAUUUGUG 2632 hsa-miR-133a UUUGGUCCCCUUCAACCAGCUG 2633 hsa-miR-141 UAACACUGUCUGGUAAAGAUGG 2634 hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCU 2635 hsa-miR-146b-5p UGAGAACUGAAUUCCAUAGGCU 2636 hsa-miR-150 UCUCCCAACCCUUGUACCAGUG 2637 hsa-miR-152 UCAGUGCAUGACAGAACUUGG 2638 hsa-miR-155 UUAAUGCUAAUCGUGAUAGGGGU 2639 hsa-miR-182 UUUGGCAAUGGUAGAACUCACACU 2640 hsa-miR-191 CAACGGAAUCCCAAAAGCAGCUG 2641 hsa-miR-19b UGUAAACAUCCUCGACUGGAAG 2642 hsa-miR-200c UAAUACUGCCGGGUAAUGAUGGA 2643 hsa-miR-205 UCCUUCAUUCCACCGGAGUCUG 2644 hsa-miR-206 UGGAAUGUAAGGAAGUGUGUGG 2645 hsa-miR-21 UAGCUUAUCAGACUGAUGUUGA 2646 hsa-miR-210 CUGUGCGUGUGACAGCGGCUGA 2647 hsa-miR-22 AAGCUGCCAGUUGAAGAACUGU 2648 hsa-miR-222 AGCUACAUCUGGCUACUGGGU 2649 hsa-miR-26a UUCAAGUAAUCCAGGAUAGGCU 2650 hsa-miR-27a UUCACAGUGGCUAAGUUCCGC 2651 hsa-miR-27b UUCACAGUGGCUAAGUUCUGC 2652 hsa-miR-29b UAGCACCAUUUGAAAUCAGUGUU 2653 hsa-miR-30a CUUUCAGUCGGAUGUUUGCAGC 2654 hsa-miR-30e-5p CUUUCAGUCGGAUGUUUACAGC 2655 hsa-miR-31 AGGCAAGAUGCUGGCAUAGCU 2656 hsa-miR-331 GCCCCUGGGCCUAUCCUAGAA 2657 hsa-miR-425 AAUGACACGAUCACUCCCGUUGA 2658 hsa-miR-449a UGGCAGUGUAUUGUUAGCUGGU 2659 hsa-miR-486-5p UCCUGUACUGAGCUGCCCCGAG 2660 hsa-miR-92a UAUUGCACUUGUCCCGGCCUGU 2661 hsa-miR-93 CAAAGUGCUGUUCGUGCAGGUAG 2662 hsa-miR-99a AACCCGUAGAUCCGAUCUUGUG 2663 

1.-20. (canceled)
 21. A method of analyzing the expression of RNA transcripts of genes in a human prostate cancer patient, comprising: obtaining a prostate tumor tissue sample from a human prostate cancer patient; extracting RNA from the tissue sample; reverse transcribing RNA transcripts of a group of genes comprising each of: BGN, COL1A1, SFRP4, FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, SRD5A2, and TPX2, and at least one reference gene, to produce cDNAs from the RNA transcripts, wherein a reference gene is a gene that does not exhibit a significantly different RNA expression level in cancerous prostate tissue compared to non-cancerous prostate tissue; and amplifying the cDNAs to produce amplicons from the cDNAs for determination of expression levels of the RNA transcripts.
 22. The method of claim 21, wherein the at least one reference gene consists of from 1 to 6 reference genes.
 23. The method of claim 21, wherein the at least one reference gene comprises one or more of AAMP, ARF1, ATP5E, CLTC, EEF1A1, GPS1, GPX1, and PGK1.
 24. The method of claim 21, wherein the at least one reference gene is selected from the group consisting of AAMP, ARF1, ATP5E, CLTC, EEF1A1, GPS1, GPX1, and PGK1.
 25. The method of claim 21, wherein the tissue sample has a positive TMPRSS2 fusion status.
 26. The method of claim 21, wherein the tissue sample has a negative TMPRSS2 fusion status.
 27. The method of claim 21, wherein the patient has early-stage prostate cancer.
 28. The method of claim 21, wherein the tissue sample comprises prostate tumor tissue with the primary Gleason pattern for the patient's prostate tumor.
 29. The method of claim 21, wherein the tissue sample comprises prostate tumor tissue with the highest Gleason pattern for the patient's prostate tumor.
 30. The method of claim 21, wherein the tissue sample comprises non-tumor prostate tissue.
 31. The method of claim 21, wherein the patient is receiving active surveillance treatment. 